--- /srv/rebuilderd/tmp/rebuilderd4Bgvqo/inputs/r-bioc-metagenomeseq_1.54.0-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderd4Bgvqo/out/r-bioc-metagenomeseq_1.54.0-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-10 15:09:23.000000 debian-binary │ --rw-r--r-- 0 0 0 2012 2026-08-10 15:09:23.000000 control.tar.xz │ --rw-r--r-- 0 0 0 2135120 2026-08-10 15:09:23.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 1932 2026-08-10 15:09:23.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 2140812 2026-08-10 15:09:23.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:09:23.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 1094 2026-08-10 15:09:23.000000 ./control │ │ │ --rw-r--r-- 0 root (0) root (0) 3519 2026-08-10 15:09:23.000000 ./md5sums │ │ │ +-rw-r--r-- 0 root (0) root (0) 960 2026-08-10 15:09:23.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 3430 2026-08-10 15:09:23.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,14 @@ │ │ │ Package: r-bioc-metagenomeseq │ │ │ Version: 1.54.0-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ -Installed-Size: 2646 │ │ │ +Installed-Size: 2647 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-bioc-biobase, r-bioc-limma, r-cran-glmnet, r-cran-rcolorbrewer, r-cran-matrixstats, r-cran-foreach, r-cran-matrix, r-cran-gplots, r-bioc-wrench, r-pkg-team-core-architecture │ │ │ -Suggests: r-bioc-annotate, r-bioc-biocgenerics, r-bioc-biomformat, r-cran-knitr, r-cran-gss, r-cran-testthat (>= 0.8), r-cran-vegan, r-bioc-ihw, r-bioc-sparsearray │ │ │ +Suggests: r-bioc-biocgenerics │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/metagenomeSeq/ │ │ │ Description: GNU R statistical analysis for sparse high-throughput sequencing │ │ │ MetagenomeSeq is designed to determine features (be it Operational │ │ │ Taxanomic Unit (OTU), species, etc.) that are differentially abundant │ │ │ between two or more groups of multiple samples. metagenomeSeq is │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ │ │ │ ├── line order │ │ │ │ @@ -5,15 +5,14 @@ │ │ │ │ usr/lib/R/site-library/metagenomeSeq/Meta/Rd.rds │ │ │ │ usr/lib/R/site-library/metagenomeSeq/Meta/data.rds │ │ │ │ usr/lib/R/site-library/metagenomeSeq/Meta/features.rds │ │ │ │ usr/lib/R/site-library/metagenomeSeq/Meta/hsearch.rds │ │ │ │ usr/lib/R/site-library/metagenomeSeq/Meta/links.rds │ │ │ │ usr/lib/R/site-library/metagenomeSeq/Meta/nsInfo.rds │ │ │ │ usr/lib/R/site-library/metagenomeSeq/Meta/package.rds │ │ │ │ -usr/lib/R/site-library/metagenomeSeq/Meta/vignette.rds │ │ │ │ usr/lib/R/site-library/metagenomeSeq/NAMESPACE │ │ │ │ usr/lib/R/site-library/metagenomeSeq/NEWS │ │ │ │ usr/lib/R/site-library/metagenomeSeq/R/metagenomeSeq │ │ │ │ usr/lib/R/site-library/metagenomeSeq/R/metagenomeSeq.rdb │ │ │ │ usr/lib/R/site-library/metagenomeSeq/R/metagenomeSeq.rdx │ │ │ │ usr/lib/R/site-library/metagenomeSeq/README.md │ │ │ │ usr/lib/R/site-library/metagenomeSeq/data/lungData.rda ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -12,44 +12,43 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 3734 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/Meta/Rd.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 172 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/Meta/data.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 123 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/Meta/features.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 3339 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/Meta/hsearch.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1597 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/Meta/links.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1179 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1590 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/Meta/package.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 304 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 2093 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 4657 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/NEWS │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/R/metagenomeSeq │ │ │ --rw-r--r-- 0 root (0) root (0) 234903 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/R/metagenomeSeq.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 2088 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/R/metagenomeSeq.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 234911 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/R/metagenomeSeq.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 2089 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/R/metagenomeSeq.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 2487 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/README.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/data/ │ │ │ -rw-r--r-- 0 root (0) root (0) 275960 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/data/lungData.rda │ │ │ -rw-r--r-- 0 root (0) root (0) 193204 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/data/mouseData.rda │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 3837 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/doc/fitTimeSeries.R │ │ │ -rw-r--r-- 0 root (0) root (0) 14420 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/doc/fitTimeSeries.Rnw │ │ │ -rw-r--r-- 0 root (0) root (0) 291599 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/doc/fitTimeSeries.pdf │ │ │ --rw-r--r-- 0 root (0) root (0) 1953 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/doc/index.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 1672 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/doc/index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 11061 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/doc/metagenomeSeq.R │ │ │ -rw-r--r-- 0 root (0) root (0) 42178 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/doc/metagenomeSeq.Rnw │ │ │ -rw-r--r-- 0 root (0) root (0) 1042960 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/doc/metagenomeSeq.pdf │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/extdata/ │ │ │ -rw-r--r-- 0 root (0) root (0) 162265 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/extdata/CHK_NAME.otus.count.csv │ │ │ -rw-r--r-- 0 root (0) root (0) 4884 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/extdata/CHK_clinical.csv │ │ │ -rw-r--r-- 0 root (0) root (0) 54501 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/extdata/CHK_otus.taxonomy.csv │ │ │ -rw-r--r-- 0 root (0) root (0) 93152 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/extdata/lungfit.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 3524 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/help/AnIndex │ │ │ -rw-r--r-- 0 root (0) root (0) 1151 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 167808 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/help/metagenomeSeq.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 2124 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/help/metagenomeSeq.rdx │ │ │ --rw-r--r-- 0 root (0) root (0) 941 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 169471 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/help/metagenomeSeq.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 2130 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/help/metagenomeSeq.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 956 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 20545 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-10 15:09:23.000000 ./usr/lib/R/site-library/metagenomeSeq/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:09:23.000000 ./usr/share/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:09:23.000000 ./usr/share/doc/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-10 15:09:23.000000 ./usr/share/doc/r-bioc-metagenomeseq/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1023 2026-08-10 15:09:23.000000 ./usr/share/doc/r-bioc-metagenomeseq/changelog.Debian.gz │ │ ├── ./usr/lib/R/site-library/metagenomeSeq/R/metagenomeSeq.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -546,15 +546,15 @@ │ │ │ │ "imports" = " median = "median", model.matrix = "model.matrix", p.adjust = "p.adjust", " │ │ │ │ "imports" = " plogis = "plogis", pnorm = "pnorm", prcomp = "prcomp", predict = "predict", " │ │ │ │ "imports" = " qlogis = "qlogis", quantile = "quantile", residuals = "residuals", " │ │ │ │ "imports" = " sd = "sd", var = "var"), utils = c(packageVersion = "packageVersion", " │ │ │ │ "imports" = " read.delim = "read.delim", read.table = "read.table", tail = "tail"" │ │ │ │ "imports" = " ))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-metagenomeseq/debian/r-bioc-metagenomeseq/usr/lib/R/site-library/metagenomeSeq"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/debian/r-bioc-metagenomeseq/usr/lib/R/site-library/metagenomeSeq"" │ │ │ │ "spec" = "c(name = "metagenomeSeq", version = "1.54.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/metagenomeSeq/R/metagenomeSeq.rdx │ │ │ ├── metagenomeSeq.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -5,456 +5,456 @@ │ │ │ │ │ $variables$.__C__fitFeatureModelResults │ │ │ │ │ [1] 3017 434 │ │ │ │ │ │ │ │ │ │ $variables$.__C__fitZigResults │ │ │ │ │ [1] 3451 531 │ │ │ │ │ │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 11864 52 │ │ │ │ │ +[1] 11872 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 12047 52 │ │ │ │ │ +[1] 12055 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__MRihw:metagenomeSeq` │ │ │ │ │ -[1] 15133 52 │ │ │ │ │ +[1] 15141 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__[:base` │ │ │ │ │ -[1] 42745 52 │ │ │ │ │ +[1] 42753 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__colMeans:base` │ │ │ │ │ -[1] 50423 53 │ │ │ │ │ +[1] 50431 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__colSums:base` │ │ │ │ │ -[1] 57688 53 │ │ │ │ │ +[1] 57696 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__libSize:metagenomeSeq` │ │ │ │ │ -[1] 60001 53 │ │ │ │ │ +[1] 60009 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__libSize<-:metagenomeSeq` │ │ │ │ │ -[1] 62725 53 │ │ │ │ │ +[1] 62733 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__normFactors:metagenomeSeq` │ │ │ │ │ -[1] 65049 53 │ │ │ │ │ +[1] 65057 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__normFactors<-:metagenomeSeq` │ │ │ │ │ -[1] 67785 53 │ │ │ │ │ +[1] 67793 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__rowMeans:base` │ │ │ │ │ -[1] 75126 53 │ │ │ │ │ +[1] 75134 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__rowSums:base` │ │ │ │ │ -[1] 82389 53 │ │ │ │ │ +[1] 82397 53 │ │ │ │ │ │ │ │ │ │ $variables$.do_fitZig │ │ │ │ │ -[1] 82442 4249 │ │ │ │ │ +[1] 82450 4249 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 86691 58 │ │ │ │ │ +[1] 86699 58 │ │ │ │ │ │ │ │ │ │ $variables$MRcoefs │ │ │ │ │ -[1] 86749 4520 │ │ │ │ │ +[1] 86757 4520 │ │ │ │ │ │ │ │ │ │ $variables$MRcounts │ │ │ │ │ -[1] 91269 1063 │ │ │ │ │ +[1] 91277 1063 │ │ │ │ │ │ │ │ │ │ $variables$MRexperiment2biom │ │ │ │ │ -[1] 92332 1690 │ │ │ │ │ +[1] 92340 1690 │ │ │ │ │ │ │ │ │ │ $variables$MRfulltable │ │ │ │ │ -[1] 94022 5229 │ │ │ │ │ +[1] 94030 5229 │ │ │ │ │ │ │ │ │ │ $variables$MRihw │ │ │ │ │ -[1] 99251 452 │ │ │ │ │ +[1] 99259 452 │ │ │ │ │ │ │ │ │ │ $variables$MRtable │ │ │ │ │ -[1] 99703 4945 │ │ │ │ │ +[1] 99711 4945 │ │ │ │ │ │ │ │ │ │ $variables$aggSamp │ │ │ │ │ -[1] 104648 331 │ │ │ │ │ +[1] 104656 331 │ │ │ │ │ │ │ │ │ │ $variables$aggTax │ │ │ │ │ -[1] 104979 496 │ │ │ │ │ +[1] 104987 496 │ │ │ │ │ │ │ │ │ │ $variables$aggregateBySample │ │ │ │ │ -[1] 105475 2465 │ │ │ │ │ +[1] 105483 2465 │ │ │ │ │ │ │ │ │ │ $variables$aggregateByTaxonomy │ │ │ │ │ -[1] 107940 3567 │ │ │ │ │ +[1] 107948 3567 │ │ │ │ │ │ │ │ │ │ $variables$biom2MRexperiment │ │ │ │ │ -[1] 111507 1811 │ │ │ │ │ +[1] 111515 1811 │ │ │ │ │ │ │ │ │ │ $variables$calcNormFactors │ │ │ │ │ -[1] 113318 1224 │ │ │ │ │ +[1] 113326 1224 │ │ │ │ │ │ │ │ │ │ $variables$calcPosComponent │ │ │ │ │ -[1] 114542 1170 │ │ │ │ │ +[1] 114550 1170 │ │ │ │ │ │ │ │ │ │ $variables$calcShrinkParameters │ │ │ │ │ -[1] 115712 1032 │ │ │ │ │ +[1] 115720 1032 │ │ │ │ │ │ │ │ │ │ $variables$calcStandardError │ │ │ │ │ -[1] 116744 4943 │ │ │ │ │ +[1] 116752 4943 │ │ │ │ │ │ │ │ │ │ $variables$calcZeroAdjustment │ │ │ │ │ -[1] 121687 1918 │ │ │ │ │ +[1] 121695 1918 │ │ │ │ │ │ │ │ │ │ $variables$calcZeroComponent │ │ │ │ │ -[1] 123605 1375 │ │ │ │ │ +[1] 123613 1375 │ │ │ │ │ │ │ │ │ │ $variables$calculateEffectiveSamples │ │ │ │ │ -[1] 124980 269 │ │ │ │ │ +[1] 124988 269 │ │ │ │ │ │ │ │ │ │ $variables$correctIndices │ │ │ │ │ -[1] 125249 985 │ │ │ │ │ +[1] 125257 985 │ │ │ │ │ │ │ │ │ │ $variables$correlationTest │ │ │ │ │ -[1] 126234 3516 │ │ │ │ │ +[1] 126242 3516 │ │ │ │ │ │ │ │ │ │ $variables$cumNorm │ │ │ │ │ -[1] 129750 942 │ │ │ │ │ +[1] 129758 942 │ │ │ │ │ │ │ │ │ │ $variables$cumNormMat │ │ │ │ │ -[1] 130692 1224 │ │ │ │ │ +[1] 130700 1224 │ │ │ │ │ │ │ │ │ │ $variables$cumNormStat │ │ │ │ │ -[1] 131916 3474 │ │ │ │ │ +[1] 131924 3474 │ │ │ │ │ │ │ │ │ │ $variables$cumNormStatFast │ │ │ │ │ -[1] 135390 3385 │ │ │ │ │ +[1] 135398 3385 │ │ │ │ │ │ │ │ │ │ $variables$deprecated_metagenomeSeq_function │ │ │ │ │ -[1] 138775 196 │ │ │ │ │ +[1] 138783 196 │ │ │ │ │ │ │ │ │ │ $variables$doCountMStep │ │ │ │ │ -[1] 138971 2638 │ │ │ │ │ +[1] 138979 2638 │ │ │ │ │ │ │ │ │ │ $variables$doEStep │ │ │ │ │ -[1] 141609 892 │ │ │ │ │ +[1] 141617 892 │ │ │ │ │ │ │ │ │ │ $variables$doZeroMStep │ │ │ │ │ -[1] 142501 1425 │ │ │ │ │ +[1] 142509 1425 │ │ │ │ │ │ │ │ │ │ $variables$expSummary │ │ │ │ │ -[1] 143926 378 │ │ │ │ │ +[1] 143934 378 │ │ │ │ │ │ │ │ │ │ $variables$exportMat │ │ │ │ │ -[1] 144304 1213 │ │ │ │ │ +[1] 144312 1213 │ │ │ │ │ │ │ │ │ │ $variables$exportStats │ │ │ │ │ -[1] 145517 2007 │ │ │ │ │ +[1] 145525 2007 │ │ │ │ │ │ │ │ │ │ $variables$extractMR │ │ │ │ │ -[1] 147524 669 │ │ │ │ │ +[1] 147532 669 │ │ │ │ │ │ │ │ │ │ $variables$filterData │ │ │ │ │ -[1] 148193 701 │ │ │ │ │ +[1] 148201 701 │ │ │ │ │ │ │ │ │ │ $variables$fitDO │ │ │ │ │ -[1] 148894 3157 │ │ │ │ │ +[1] 148902 3157 │ │ │ │ │ │ │ │ │ │ $variables$fitFeatureModel │ │ │ │ │ -[1] 152051 3932 │ │ │ │ │ +[1] 152059 3932 │ │ │ │ │ │ │ │ │ │ $variables$fitLogNormal │ │ │ │ │ -[1] 155983 2609 │ │ │ │ │ +[1] 155991 2609 │ │ │ │ │ │ │ │ │ │ $variables$fitMeta │ │ │ │ │ -[1] 158592 300 │ │ │ │ │ +[1] 158600 300 │ │ │ │ │ │ │ │ │ │ $variables$fitMultipleTimeSeries │ │ │ │ │ -[1] 158892 1286 │ │ │ │ │ +[1] 158900 1286 │ │ │ │ │ │ │ │ │ │ $variables$fitPA │ │ │ │ │ -[1] 160178 3431 │ │ │ │ │ +[1] 160186 3431 │ │ │ │ │ │ │ │ │ │ $variables$fitSSTimeSeries │ │ │ │ │ -[1] 163609 4735 │ │ │ │ │ +[1] 163617 4735 │ │ │ │ │ │ │ │ │ │ $variables$fitTimeSeries │ │ │ │ │ -[1] 168344 1037 │ │ │ │ │ +[1] 168352 1037 │ │ │ │ │ │ │ │ │ │ $variables$fitZeroLogNormal │ │ │ │ │ -[1] 169381 6403 │ │ │ │ │ +[1] 169389 6403 │ │ │ │ │ │ │ │ │ │ $variables$fitZig │ │ │ │ │ -[1] 175784 2897 │ │ │ │ │ +[1] 175792 2897 │ │ │ │ │ │ │ │ │ │ $variables$getCountDensity │ │ │ │ │ -[1] 178681 264 │ │ │ │ │ +[1] 178689 264 │ │ │ │ │ │ │ │ │ │ $variables$getEpsilon │ │ │ │ │ -[1] 178945 408 │ │ │ │ │ +[1] 178953 408 │ │ │ │ │ │ │ │ │ │ $variables$getNegativeLogLikelihoods │ │ │ │ │ -[1] 179353 789 │ │ │ │ │ +[1] 179361 789 │ │ │ │ │ │ │ │ │ │ $variables$getPi │ │ │ │ │ -[1] 180142 234 │ │ │ │ │ +[1] 180150 234 │ │ │ │ │ │ │ │ │ │ $variables$getZ │ │ │ │ │ -[1] 180376 870 │ │ │ │ │ +[1] 180384 870 │ │ │ │ │ │ │ │ │ │ $variables$isItStillActive │ │ │ │ │ -[1] 181246 739 │ │ │ │ │ +[1] 181254 739 │ │ │ │ │ │ │ │ │ │ $variables$libSize │ │ │ │ │ -[1] 181985 440 │ │ │ │ │ +[1] 181993 440 │ │ │ │ │ │ │ │ │ │ $variables$`libSize<-` │ │ │ │ │ -[1] 182425 463 │ │ │ │ │ +[1] 182433 463 │ │ │ │ │ │ │ │ │ │ $variables$loadBiom │ │ │ │ │ -[1] 182888 443 │ │ │ │ │ +[1] 182896 443 │ │ │ │ │ │ │ │ │ │ $variables$loadMeta │ │ │ │ │ -[1] 183331 1026 │ │ │ │ │ +[1] 183339 1026 │ │ │ │ │ │ │ │ │ │ $variables$loadMetaQ │ │ │ │ │ -[1] 184357 1328 │ │ │ │ │ +[1] 184365 1328 │ │ │ │ │ │ │ │ │ │ $variables$loadPhenoData │ │ │ │ │ -[1] 185685 1952 │ │ │ │ │ +[1] 185693 1952 │ │ │ │ │ │ │ │ │ │ $variables$load_biom │ │ │ │ │ -[1] 187637 295 │ │ │ │ │ +[1] 187645 295 │ │ │ │ │ │ │ │ │ │ $variables$load_meta │ │ │ │ │ -[1] 187932 295 │ │ │ │ │ +[1] 187940 295 │ │ │ │ │ │ │ │ │ │ $variables$load_metaQ │ │ │ │ │ -[1] 188227 295 │ │ │ │ │ +[1] 188235 295 │ │ │ │ │ │ │ │ │ │ $variables$load_phenoData │ │ │ │ │ -[1] 188522 299 │ │ │ │ │ +[1] 188530 299 │ │ │ │ │ │ │ │ │ │ $variables$makeLabels │ │ │ │ │ -[1] 188821 665 │ │ │ │ │ +[1] 188829 665 │ │ │ │ │ │ │ │ │ │ $variables$mergeMRexperiments │ │ │ │ │ -[1] 189486 2582 │ │ │ │ │ +[1] 189494 2582 │ │ │ │ │ │ │ │ │ │ $variables$mergeTable │ │ │ │ │ -[1] 192068 986 │ │ │ │ │ +[1] 192076 986 │ │ │ │ │ │ │ │ │ │ $variables$metadata │ │ │ │ │ -[1] 193054 2268 │ │ │ │ │ +[1] 193062 2268 │ │ │ │ │ │ │ │ │ │ $variables$newMRexperiment │ │ │ │ │ -[1] 195322 1620 │ │ │ │ │ +[1] 195330 1620 │ │ │ │ │ │ │ │ │ │ $variables$normFactors │ │ │ │ │ -[1] 196942 442 │ │ │ │ │ +[1] 196950 442 │ │ │ │ │ │ │ │ │ │ $variables$`normFactors<-` │ │ │ │ │ -[1] 197384 465 │ │ │ │ │ +[1] 197392 465 │ │ │ │ │ │ │ │ │ │ $variables$plotBubble │ │ │ │ │ -[1] 197849 4814 │ │ │ │ │ +[1] 197857 4814 │ │ │ │ │ │ │ │ │ │ $variables$plotClassTimeSeries │ │ │ │ │ -[1] 202663 1999 │ │ │ │ │ +[1] 202671 1999 │ │ │ │ │ │ │ │ │ │ $variables$plotCorr │ │ │ │ │ -[1] 204662 1197 │ │ │ │ │ +[1] 204670 1197 │ │ │ │ │ │ │ │ │ │ $variables$plotFeature │ │ │ │ │ -[1] 205859 2380 │ │ │ │ │ +[1] 205867 2380 │ │ │ │ │ │ │ │ │ │ $variables$plotGenus │ │ │ │ │ -[1] 208239 1994 │ │ │ │ │ +[1] 208247 1994 │ │ │ │ │ │ │ │ │ │ $variables$plotMRheatmap │ │ │ │ │ -[1] 210233 889 │ │ │ │ │ +[1] 210241 889 │ │ │ │ │ │ │ │ │ │ $variables$plotOTU │ │ │ │ │ -[1] 211122 2054 │ │ │ │ │ +[1] 211130 2054 │ │ │ │ │ │ │ │ │ │ $variables$plotOrd │ │ │ │ │ -[1] 213176 2683 │ │ │ │ │ +[1] 213184 2683 │ │ │ │ │ │ │ │ │ │ $variables$plotRare │ │ │ │ │ -[1] 215859 1295 │ │ │ │ │ +[1] 215867 1295 │ │ │ │ │ │ │ │ │ │ $variables$plotTimeSeries │ │ │ │ │ -[1] 217154 1994 │ │ │ │ │ +[1] 217162 1994 │ │ │ │ │ │ │ │ │ │ $variables$posteriorProbs │ │ │ │ │ -[1] 219148 370 │ │ │ │ │ +[1] 219156 370 │ │ │ │ │ │ │ │ │ │ $variables$returnAppropriateObj │ │ │ │ │ -[1] 219518 608 │ │ │ │ │ +[1] 219526 608 │ │ │ │ │ │ │ │ │ │ $variables$ssFit │ │ │ │ │ -[1] 220126 1376 │ │ │ │ │ +[1] 220134 1376 │ │ │ │ │ │ │ │ │ │ $variables$ssIntervalCandidate │ │ │ │ │ -[1] 221502 2135 │ │ │ │ │ +[1] 221510 2135 │ │ │ │ │ │ │ │ │ │ $variables$ssPerm │ │ │ │ │ -[1] 223637 873 │ │ │ │ │ +[1] 223645 873 │ │ │ │ │ │ │ │ │ │ $variables$ssPermAnalysis │ │ │ │ │ -[1] 224510 2162 │ │ │ │ │ +[1] 224518 2162 │ │ │ │ │ │ │ │ │ │ $variables$trapz │ │ │ │ │ -[1] 226672 1582 │ │ │ │ │ +[1] 226680 1582 │ │ │ │ │ │ │ │ │ │ $variables$ts2MRexperiment │ │ │ │ │ -[1] 228254 3295 │ │ │ │ │ +[1] 228262 3295 │ │ │ │ │ │ │ │ │ │ $variables$uniqueFeatures │ │ │ │ │ -[1] 231549 1997 │ │ │ │ │ +[1] 231557 1997 │ │ │ │ │ │ │ │ │ │ $variables$wrenchNorm │ │ │ │ │ -[1] 233546 529 │ │ │ │ │ +[1] 233554 529 │ │ │ │ │ │ │ │ │ │ $variables$zigControl │ │ │ │ │ -[1] 234075 828 │ │ │ │ │ +[1] 234083 828 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 4276 7588 │ │ │ │ │ +[1] 4276 7596 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 40983 256 │ │ │ │ │ +[1] 40991 256 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 15461 12761 │ │ │ │ │ +[1] 15469 12761 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 15185 276 │ │ │ │ │ +[1] 15193 276 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 28222 12761 │ │ │ │ │ +[1] 28230 12761 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 49920 503 │ │ │ │ │ +[1] 49928 503 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 49353 567 │ │ │ │ │ +[1] 49361 567 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 42965 3110 │ │ │ │ │ +[1] 42973 3110 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 42797 168 │ │ │ │ │ +[1] 42805 168 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 46075 3110 │ │ │ │ │ +[1] 46083 3110 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 49185 168 │ │ │ │ │ +[1] 49193 168 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 3982 131 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 57185 503 │ │ │ │ │ +[1] 57193 503 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 56618 567 │ │ │ │ │ +[1] 56626 567 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 50476 3071 │ │ │ │ │ +[1] 50484 3071 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 53547 3071 │ │ │ │ │ +[1] 53555 3071 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 59335 666 │ │ │ │ │ +[1] 59343 666 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 59073 262 │ │ │ │ │ +[1] 59081 262 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ -[1] 57741 666 │ │ │ │ │ +[1] 57749 666 │ │ │ │ │ │ │ │ │ │ $references$`env::27` │ │ │ │ │ -[1] 58407 666 │ │ │ │ │ +[1] 58415 666 │ │ │ │ │ │ │ │ │ │ $references$`env::28` │ │ │ │ │ -[1] 61924 801 │ │ │ │ │ +[1] 61932 801 │ │ │ │ │ │ │ │ │ │ $references$`env::29` │ │ │ │ │ -[1] 61656 268 │ │ │ │ │ +[1] 61664 268 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 4113 163 │ │ │ │ │ │ │ │ │ │ $references$`env::30` │ │ │ │ │ -[1] 60054 801 │ │ │ │ │ +[1] 60062 801 │ │ │ │ │ │ │ │ │ │ $references$`env::31` │ │ │ │ │ -[1] 60855 801 │ │ │ │ │ +[1] 60863 801 │ │ │ │ │ │ │ │ │ │ $references$`env::32` │ │ │ │ │ -[1] 64380 669 │ │ │ │ │ +[1] 64388 669 │ │ │ │ │ │ │ │ │ │ $references$`env::33` │ │ │ │ │ -[1] 64116 264 │ │ │ │ │ +[1] 64124 264 │ │ │ │ │ │ │ │ │ │ $references$`env::34` │ │ │ │ │ -[1] 62778 669 │ │ │ │ │ +[1] 62786 669 │ │ │ │ │ │ │ │ │ │ $references$`env::35` │ │ │ │ │ -[1] 63447 669 │ │ │ │ │ +[1] 63455 669 │ │ │ │ │ │ │ │ │ │ $references$`env::36` │ │ │ │ │ -[1] 66980 805 │ │ │ │ │ +[1] 66988 805 │ │ │ │ │ │ │ │ │ │ $references$`env::37` │ │ │ │ │ -[1] 66712 268 │ │ │ │ │ +[1] 66720 268 │ │ │ │ │ │ │ │ │ │ $references$`env::38` │ │ │ │ │ -[1] 65102 805 │ │ │ │ │ +[1] 65110 805 │ │ │ │ │ │ │ │ │ │ $references$`env::39` │ │ │ │ │ -[1] 65907 805 │ │ │ │ │ +[1] 65915 805 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 11916 131 │ │ │ │ │ +[1] 11924 131 │ │ │ │ │ │ │ │ │ │ $references$`env::40` │ │ │ │ │ -[1] 74622 504 │ │ │ │ │ +[1] 74630 504 │ │ │ │ │ │ │ │ │ │ $references$`env::41` │ │ │ │ │ -[1] 74050 572 │ │ │ │ │ +[1] 74058 572 │ │ │ │ │ │ │ │ │ │ $references$`env::42` │ │ │ │ │ -[1] 67838 3106 │ │ │ │ │ +[1] 67846 3106 │ │ │ │ │ │ │ │ │ │ $references$`env::43` │ │ │ │ │ -[1] 70944 3106 │ │ │ │ │ +[1] 70952 3106 │ │ │ │ │ │ │ │ │ │ $references$`env::44` │ │ │ │ │ -[1] 81886 503 │ │ │ │ │ +[1] 81894 503 │ │ │ │ │ │ │ │ │ │ $references$`env::45` │ │ │ │ │ -[1] 81315 571 │ │ │ │ │ +[1] 81323 571 │ │ │ │ │ │ │ │ │ │ $references$`env::46` │ │ │ │ │ -[1] 75179 3068 │ │ │ │ │ +[1] 75187 3068 │ │ │ │ │ │ │ │ │ │ $references$`env::47` │ │ │ │ │ -[1] 78247 3068 │ │ │ │ │ +[1] 78255 3068 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 14208 925 │ │ │ │ │ +[1] 14216 925 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 13949 259 │ │ │ │ │ +[1] 13957 259 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 12099 925 │ │ │ │ │ +[1] 12107 925 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 13024 925 │ │ │ │ │ +[1] 13032 925 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 41239 1506 │ │ │ │ │ +[1] 41247 1506 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/metagenomeSeq/doc/index.html │ │ │ @@ -10,26 +10,21 @@ │ │ │ │ │ │
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│ │ │

Vignettes from package 'metagenomeSeq'

│ │ │ +The package contains no vignette meta-information. │ │ │ +

Other files in the doc directory

│ │ │ │ │ │ -│ │ │ -│ │ │ +│ │ │ │ │ │ -│ │ │ -│ │ │ -│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ +│ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │ + │ │ │
metagenomeSeq::fitTimeSeriesfitTimeSeries: differential abundance analysis through time or locationPDFsourceR code
metagenomeSeq::metagenomeSeqmetagenomeSeq: statistical analysis for sparse high-throughput sequencingPDFsourceR code
fitTimeSeries.R
fitTimeSeries.Rnw
fitTimeSeries.pdf
metagenomeSeq.R
metagenomeSeq.Rnw
metagenomeSeq.pdf
│ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,10 +1,12 @@ │ │ │ │ ************ VViiggnneetttteess aanndd ootthheerr ddooccuummeennttaattiioonn[[[[RR llooggoo]]]] ************ │ │ │ │ =============================================================================== │ │ │ │ _[_[_U_p_]_]_[_[_T_o_p_]_] │ │ │ │ ********** VViiggnneetttteess ffrroomm ppaacckkaaggee ''mmeettaaggeennoommeeSSeeqq'' ********** │ │ │ │ -_m_e_t_a_g_e_n_o_m_e_S_e_q_:_:_f_i_t_T_i_m_e_S_e_r_i_e_s fitTimeSeries: differential _P_D_F _s_o_u_r_c_e _R_ _c_o_d_e │ │ │ │ - abundance analysis through time │ │ │ │ - or location │ │ │ │ -_m_e_t_a_g_e_n_o_m_e_S_e_q_:_:_m_e_t_a_g_e_n_o_m_e_S_e_q metagenomeSeq: statistical _P_D_F _s_o_u_r_c_e _R_ _c_o_d_e │ │ │ │ - analysis for sparse high- │ │ │ │ - throughput sequencing │ │ │ │ +The package contains no vignette meta-information. │ │ │ │ +********** OOtthheerr ffiilleess iinn tthhee ddoocc ddiirreeccttoorryy ********** │ │ │ │ + _f_i_t_T_i_m_e_S_e_r_i_e_s_._R │ │ │ │ + _f_i_t_T_i_m_e_S_e_r_i_e_s_._R_n_w │ │ │ │ + _f_i_t_T_i_m_e_S_e_r_i_e_s_._p_d_f │ │ │ │ + _m_e_t_a_g_e_n_o_m_e_S_e_q_._R │ │ │ │ + _m_e_t_a_g_e_n_o_m_e_S_e_q_._R_n_w │ │ │ │ + _m_e_t_a_g_e_n_o_m_e_S_e_q_._p_d_f │ │ ├── ./usr/lib/R/site-library/metagenomeSeq/help/metagenomeSeq.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -85,15 +85,15 @@ │ │ │ │ structure("lungTrim=cumNorm(lungTrim,p=0.5)\n", Rd_tag = "RCODE"), │ │ │ │ structure("smokingStatus = pData(lungTrim)$SmokingStatus\n", Rd_tag = "RCODE"), │ │ │ │ structure("mod = model.matrix(~smokingStatus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("fit = fitZig(obj = lungTrim,mod=mod)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(MRcoefs(fit))\n", Rd_tag = "RCODE"), │ │ │ │ structure("####\n", Rd_tag = "RCODE"), structure("fit = fitFeatureModel(obj = lungTrim,mod=mod)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(MRcoefs(fit))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRcoefs.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/MRcoefs.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ MRcounts (list) = structure(list(structure(list(structure("Accessor for the counts slot of a MRexperiment object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("MRcounts", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("MRcounts", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("MRcounts,MRexperiment-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The counts slot holds the raw count data representing (along the rows) the\n", Rd_tag = "TEXT"), │ │ │ │ @@ -114,15 +114,15 @@ │ │ │ │ structure(list(list(structure("sl", Rd_tag = "TEXT")), │ │ │ │ list(structure("The value to scale by (default=1000).", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Normalized or raw counts\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Joseph N. Paulson, jpaulson@umiacs.umd.edu\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(lungData)\n", Rd_tag = "RCODE"), structure("head(MRcounts(lungData))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRcounts.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/MRcounts.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ MRexperiment-class (list) = structure(list(structure(list(structure("Class \"MRexperiment\" -- a modified eSet object for the data from high-throughput sequencing experiments", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("MRexperiment", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("MRexperiment-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("[,MRexperiment,ANY,ANY,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("[,MRexperiment-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -198,15 +198,15 @@ │ │ │ │ structure("MRexperiment", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" is derived from the virtual class,", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("eSet", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" and thereby has a ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("phenoData", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" slot which allows for sample annotation. In the phenoData data frame factors are stored. The normalization factors and library size information is stored in a slot called expSummary that is an annotated data frame and is repopulated for subsetted data.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\note"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("# See vignette\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRexperiment-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("# See vignette\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/MRexperiment-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ MRexperiment2biom (list) = structure(list(structure(list(structure("MRexperiment to biom objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("MRexperiment2biom", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("MRexperiment2biom", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Wrapper to convert MRexperiment objects to biom objects.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("MRexperiment2biom(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -239,15 +239,15 @@ │ │ │ │ structure("loadPhenoData", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("newMRexperiment", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("loadBiom", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("biom2MRexperiment", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRexperiment2biom.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/MRexperiment2biom.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ MRfulltable (list) = structure(list(structure(list(structure("Table of top microbial marker gene from linear model fit including sequence\n", Rd_tag = "TEXT"), │ │ │ │ structure("information", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("MRfulltable", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("MRfulltable", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Extract a table of the top-ranked features from a linear model fit. This\n", Rd_tag = "TEXT"), │ │ │ │ @@ -332,28 +332,28 @@ │ │ │ │ structure("lungTrim=cumNorm(lungTrim,p=0.5)\n", Rd_tag = "RCODE"), │ │ │ │ structure("smokingStatus = pData(lungTrim)$SmokingStatus\n", Rd_tag = "RCODE"), │ │ │ │ structure("mod = model.matrix(~smokingStatus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("fit = fitZig(obj = lungTrim,mod=mod)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(MRfulltable(fit))\n", Rd_tag = "RCODE"), │ │ │ │ structure("####\n", Rd_tag = "RCODE"), structure("fit = fitFeatureModel(obj = lungTrim,mod=mod)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(MRfulltable(fit))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRfulltable.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/MRfulltable.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ MRihw (list) = structure(list(structure(list(structure("MRihw runs IHW within a MRcoefs() call", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("MRihw", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("MRihw", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Function used in MRcoefs() when \"IHW\" is set as the p value adjustment method\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("MRihw(obj, ...)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("obj", Rd_tag = "TEXT")), list(structure("Either a fitFeatureModelResults or fitZigResults object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("...", Rd_tag = "TEXT")), │ │ │ │ list(structure("other parameters", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRihw.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/MRihw.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ MRihw-fitFeatureModelResults (list) = structure(list(structure(list(structure("MRihw runs IHW within a MRcoefs() call", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("MRihw,fitFeatureModelResults-method", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("MRihw,fitFeatureModelResults-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Function used in MRcoefs() when \"IHW\" is set as the p value adjustment method\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(list( │ │ │ │ @@ -372,15 +372,15 @@ │ │ │ │ structure(", options are \"ihw-abundance\" (median feature count per row) \n", Rd_tag = "TEXT"), │ │ │ │ structure("and \"ihw-ubiquity\" (number of non-zero features per row). For obj of class ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("fitZigResults-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", \n", Rd_tag = "TEXT"), structure("options are \"ihw-abundance\" (weighted mean per feature) and \"ihw-ubiquity\" (number of non-zero features per row).", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("alpha", Rd_tag = "TEXT")), │ │ │ │ list(structure("pvalue significance level specified for IHW call. Default is 0.1", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRihw-fitFeatureModelResults.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/MRihw-fitFeatureModelResults.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ MRihw-fitZigResults (list) = structure(list(structure(list(structure("MRihw runs IHW within a MRcoefs() call", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("MRihw,fitZigResults-method", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("MRihw,fitZigResults-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Function used in MRcoefs() when \"IHW\" is set as the p value adjustment method\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(list( │ │ │ │ @@ -399,15 +399,15 @@ │ │ │ │ structure(", options are \"ihw-abundance\" (median feature count per row) \n", Rd_tag = "TEXT"), │ │ │ │ structure("and \"ihw-ubiquity\" (number of non-zero features per row). For obj of class ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("fitZigResults-class", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(", \n", Rd_tag = "TEXT"), structure("options are \"ihw-abundance\" (weighted mean per feature) and \"ihw-ubiquity\" (number of non-zero features per row).", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("alpha", Rd_tag = "TEXT")), │ │ │ │ list(structure("pvalue significance level specified for IHW call. Default is 0.1", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRihw-fitZigResults.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/MRihw-fitZigResults.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ MRtable (list) = structure(list(structure(list(structure("Table of top microbial marker gene from linear model fit including sequence\n", Rd_tag = "TEXT"), │ │ │ │ structure("information", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("MRtable", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("MRtable", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Extract a table of the top-ranked features from a linear model fit. This\n", Rd_tag = "TEXT"), │ │ │ │ @@ -490,15 +490,15 @@ │ │ │ │ structure("lungTrim=cumNorm(lungTrim,p=0.5)\n", Rd_tag = "RCODE"), │ │ │ │ structure("smokingStatus = pData(lungTrim)$SmokingStatus\n", Rd_tag = "RCODE"), │ │ │ │ structure("mod = model.matrix(~smokingStatus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("fit = fitZig(obj = lungTrim,mod=mod)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(MRtable(fit))\n", Rd_tag = "RCODE"), │ │ │ │ structure("####\n", Rd_tag = "RCODE"), structure("fit = fitFeatureModel(obj = lungTrim,mod=mod)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(MRtable(fit))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRtable.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/MRtable.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ aggregateBySample (list) = structure(list(structure(list(structure("Aggregates a MRexperiment object or counts matrix to by a factor.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("aggregateBySample", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("aggregateBySample", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("aggSamp", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Using the phenoData information in the MRexperiment, calling aggregateBySample on a\n", Rd_tag = "TEXT"), │ │ │ │ @@ -520,15 +520,15 @@ │ │ │ │ list(structure("Either 'MRexperiment' or 'matrix'", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An aggregated count matrix or MRexperiment object where the new pData is a vector of `fct` levels.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("aggregateBySample(mouseData[1:100,],fct=\"diet\",aggfun=rowSums)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# not run\n", Rd_tag = "RCODE"), structure("# aggregateBySample(mouseData,fct=\"diet\",aggfun=matrixStats::rowMedians)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# aggSamp(mouseData,fct='diet',aggfun=rowMaxs)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/aggregateBySample.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/aggregateBySample.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ aggregateByTaxonomy (list) = structure(list(structure(list(structure("Aggregates a MRexperiment object or counts matrix to a particular level.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("aggregateByTaxonomy", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("aggregateByTaxonomy", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("aggTax", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Using the featureData information in the MRexperiment, calling aggregateByTaxonomy on a\n", Rd_tag = "TEXT"), │ │ │ │ @@ -583,15 +583,15 @@ │ │ │ │ list(structure("Either 'MRexperiment' or 'matrix'", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An aggregated count matrix.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("aggregateByTaxonomy(mouseData[1:100,],lvl=\"class\",norm=TRUE,aggfun=colSums)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# not run\n", Rd_tag = "RCODE"), structure("# aggregateByTaxonomy(mouseData,lvl=\"class\",norm=TRUE,aggfun=colMedians)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# aggTax(mouseData,lvl='phylum',norm=FALSE,aggfun=colSums)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/aggregateByTaxonomy.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/aggregateByTaxonomy.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ biom2MRexperiment (list) = structure(list(structure(list(structure("Biom to MRexperiment objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("biom2MRexperiment", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("biom2MRexperiment", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Wrapper to convert biom files to MRexperiment objects.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("biom2MRexperiment(obj)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -609,15 +609,15 @@ │ │ │ │ structure("loadBiom", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(biomformat)\n", Rd_tag = "RCODE"), │ │ │ │ structure("rich_dense_file = system.file(\"extdata\", \"rich_dense_otu_table.biom\", package = \"biomformat\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("x = biomformat::read_biom(rich_dense_file)\n", Rd_tag = "RCODE"), │ │ │ │ structure("biom2MRexperiment(x)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/biom2MRexperiment.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/biom2MRexperiment.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calcNormFactors (list) = structure(list(structure(list(structure("Cumulative sum scaling (css) normalization factors", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcNormFactors", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcNormFactors", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Return a vector of the the sum up to and including a quantile.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("calcNormFactors(obj, p = cumNormStatFast(obj))\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -633,15 +633,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("cumNormStatFast", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("cumNorm", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("head(calcNormFactors(mouseData))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calcNormFactors.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/calcNormFactors.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calcPosComponent (list) = structure(list(structure(list(structure("Positive component", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcPosComponent", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcPosComponent", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Fit the positive (log-normal) component\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("calcPosComponent(mat, mod, weights)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -654,15 +654,15 @@ │ │ │ │ structure(list(list(structure("weights", Rd_tag = "TEXT")), │ │ │ │ list(structure("Weight matrix for samples and counts", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZeroLogNormal", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("fitFeatureModel", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calcPosComponent.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/calcPosComponent.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calcShrinkParameters (list) = structure(list(structure(list(structure("Calculate shrinkage parameters", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcShrinkParameters", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcShrinkParameters", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the shrunken variances and variance of parameters of interest across features.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("calcShrinkParameters(fit, coef, mins2, exclude = NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -678,15 +678,15 @@ │ │ │ │ structure(list(list(structure("exclude", Rd_tag = "TEXT")), │ │ │ │ list(structure("Vector of features to exclude when shrinking", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZeroLogNormal", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("fitFeatureModel", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calcShrinkParameters.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/calcShrinkParameters.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calcStandardError (list) = structure(list(structure(list(structure("Calculate the zero-inflated log-normal statistic's standard error", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcStandardError", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcStandardError", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculat the se for the model. Code modified from\n", Rd_tag = "TEXT"), │ │ │ │ structure("\"Adjusting for covariates in zero-inflated gamma and \n", Rd_tag = "TEXT"), │ │ │ │ @@ -707,15 +707,15 @@ │ │ │ │ structure(list(list(structure("exclude", Rd_tag = "TEXT")), │ │ │ │ list(structure("List of features to exclude", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZeroLogNormal", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("fitFeatureModel", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calcStandardError.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/calcStandardError.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calcZeroAdjustment (list) = structure(list(structure(list(structure("Calculate the zero-inflated component's adjustment factor", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcZeroAdjustment", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcZeroAdjustment", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the log ratio of average marginal probabilities for each sample\n", Rd_tag = "TEXT"), │ │ │ │ structure("having a positive count. This becomes the adjustment factor for the log \n", Rd_tag = "TEXT"), │ │ │ │ @@ -736,15 +736,15 @@ │ │ │ │ structure(list(list(structure("exclude", Rd_tag = "TEXT")), │ │ │ │ list(structure("List of features to exclude", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZeroLogNormal", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("fitFeatureModel", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calcZeroAdjustment.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/calcZeroAdjustment.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calcZeroComponent (list) = structure(list(structure(list(structure("Zero component", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calcZeroComponent", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calcZeroComponent", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Fit the zero (logisitic) component\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("calcZeroComponent(mat, mod, weights)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -757,15 +757,15 @@ │ │ │ │ structure(list(list(structure("weights", Rd_tag = "TEXT")), │ │ │ │ list(structure("Weight matrix for samples and counts", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZeroLogNormal", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("fitFeatureModel", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calcZeroComponent.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/calcZeroComponent.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calculateEffectiveSamples (list) = structure(list(structure(list(structure("Estimated effective samples per feature", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calculateEffectiveSamples", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calculateEffectiveSamples", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculates the number of estimated effective samples per feature from the output\n", Rd_tag = "TEXT"), │ │ │ │ structure("of a fitZig run. The estimated effective samples per feature is calculated as the\n", Rd_tag = "TEXT"), │ │ │ │ @@ -778,15 +778,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A list of the estimated effective samples per feature.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("MRcoefs", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("MRfulltable", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calculateEffectiveSamples.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/calculateEffectiveSamples.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ correctIndices (list) = structure(list(structure(list(structure("Calculate the correct indices for the output of correlationTest", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("correctIndices", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("correctIndices", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Consider the upper triangular portion of a matrix of size nxn. Results from the ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("correlationTest", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ @@ -804,15 +804,15 @@ │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("mat = MRcounts(mouseData)[55:60,]\n", Rd_tag = "RCODE"), │ │ │ │ structure("cors = correlationTest(mat)\n", Rd_tag = "RCODE"), │ │ │ │ structure("ind = correctIndices(nrow(mat))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("cormat = as.matrix(dist(mat))\n", Rd_tag = "RCODE"), │ │ │ │ structure("cormat[cormat>0] = 0\n", Rd_tag = "RCODE"), │ │ │ │ structure("cormat[upper.tri(cormat)][ind] = cors[,1]\n", Rd_tag = "RCODE"), │ │ │ │ structure("table(cormat[1,-1] - cors[1:5,1])\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/correctIndices.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/correctIndices.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ correlationTest (list) = structure(list(structure(list(structure("Correlation of each row of a matrix or MRexperiment object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("correlationTest", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("correlationTest", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("corTest", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculates the (pairwise) correlation statistics and associated p-values of a matrix\n", Rd_tag = "TEXT"), │ │ │ │ @@ -863,15 +863,15 @@ │ │ │ │ structure("cormat = as.matrix(dist(mat)) # Creating a matrix\n", Rd_tag = "RCODE"), │ │ │ │ structure("cormat[cormat>0] = 0 # Creating an empty matrix\n", Rd_tag = "RCODE"), │ │ │ │ structure("ind = correctIndices(nrow(mat))\n", Rd_tag = "RCODE"), │ │ │ │ structure("cormat[upper.tri(cormat)][ind] = cors[,1] \n", Rd_tag = "RCODE"), │ │ │ │ structure("table(cormat[1,-1] - cors[1:9,1])\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Correlation of raw counts with a vector (library size in this case)\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("cors = correlationTest(mouseData[1:10,],libSize(mouseData),norm=FALSE,log=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("head(cors)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/correlationTest.Rd", class = "Rd", meta = list( │ │ │ │ + structure("head(cors)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/correlationTest.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ cumNorm (list) = structure(list(structure(list(structure("Cumulative sum scaling normalization", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("cumNorm", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("cumNorm", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculates each column's quantile and calculates the sum up to and including\n", Rd_tag = "TEXT"), │ │ │ │ structure("that quantile.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -888,15 +888,15 @@ │ │ │ │ structure(list(structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("cumNormStat", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("mouseData <- cumNorm(mouseData)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(normFactors(mouseData))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/cumNorm.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/cumNorm.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ cumNormMat (list) = structure(list(structure(list(structure("Cumulative sum scaling factors.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("cumNormMat", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("cumNormMat", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculates each column's quantile and calculates the sum up to and including\n", Rd_tag = "TEXT"), │ │ │ │ structure("that quantile.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -915,15 +915,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("cumNorm", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("head(cumNormMat(mouseData))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/cumNormMat.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/cumNormMat.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ cumNormStat (list) = structure(list(structure(list(structure("Cumulative sum scaling percentile selection", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("cumNormStat", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("cumNormStat", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculates the percentile for which to sum counts up to and scale by.\n", Rd_tag = "TEXT"), │ │ │ │ structure("cumNormStat might be deprecated one day. Deviates from methods in Nature Methods paper\n", Rd_tag = "TEXT"), │ │ │ │ @@ -952,15 +952,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("cumNorm", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("cumNormStatFast", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("p = round(cumNormStat(mouseData,pFlag=FALSE),digits=2)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/cumNormStat.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/cumNormStat.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ cumNormStatFast (list) = structure(list(structure(list(structure("Cumulative sum scaling percentile selection", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("cumNormStatFast", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("cumNormStatFast", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculates the percentile for which to sum counts up to and scale by. Faster\n", Rd_tag = "TEXT"), │ │ │ │ structure("version than available in cumNormStat. Deviates from methods described in Nature Methods by\n", Rd_tag = "TEXT"), │ │ │ │ @@ -985,15 +985,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("cumNorm", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("cumNormStat", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("p = round(cumNormStatFast(mouseData,pFlag=FALSE),digits=2)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/cumNormStatFast.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/cumNormStatFast.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ doCountMStep (list) = structure(list(structure(list(structure("Compute the Maximization step calculation for features still active.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("doCountMStep", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("doCountMStep", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Maximization step is solved by weighted least squares. The function also\n", Rd_tag = "TEXT"), │ │ │ │ structure("computes counts residuals.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1026,15 +1026,15 @@ │ │ │ │ structure("$(1-delta_ij) log f_count(y;mu_i,sigma_i^2 )+delta_ij log\n", Rd_tag = "TEXT"), │ │ │ │ structure("pi_j(s_j)+(1-delta_ij)log (1-pi_j (s_j))$. The responsibilities are defined\n", Rd_tag = "TEXT"), │ │ │ │ structure("as $z_ij = pr(delta_ij=1 | data)$.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Update matrix (m x n) of estimate responsibilities (probabilities\n", Rd_tag = "TEXT"), │ │ │ │ structure("that a count comes from a spike distribution at 0).\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/doCountMStep.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/doCountMStep.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ doEStep (list) = structure(list(structure(list(structure("Compute the Expectation step.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("doEStep", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("doEStep", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Estimates the responsibilities $z_ij = fracpi_j cdot I_0(y_ijpi_j cdot\n", Rd_tag = "TEXT"), │ │ │ │ structure("I_0(y_ij + (1-pi_j) cdot f_count(y_ij\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1057,15 +1057,15 @@ │ │ │ │ structure("$(1-delta_ij) log f_count(y;mu_i,sigma_i^2 )+delta_ij log\n", Rd_tag = "TEXT"), │ │ │ │ structure("pi_j(s_j)+(1-delta_ij)log (1-pi_j (sj))$. The responsibilities are defined\n", Rd_tag = "TEXT"), │ │ │ │ structure("as $z_ij = pr(delta_ij=1 | data)$.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Updated matrix (m x n) of estimate responsibilities (probabilities\n", Rd_tag = "TEXT"), │ │ │ │ structure("that a count comes from a spike distribution at 0).\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/doEStep.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/doEStep.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ doZeroMStep (list) = structure(list(structure(list(structure("Compute the zero Maximization step.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("doZeroMStep", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("doZeroMStep", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Performs Maximization step calculation for the mixture components. Uses\n", Rd_tag = "TEXT"), │ │ │ │ structure("least squares to fit the parameters of the mean of the logistic\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1090,15 +1090,15 @@ │ │ │ │ structure("the number of OTUs observed as a linear effect of the depth of coverage.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("List of the zero fit (zero mean model) coefficients, variance -\n", Rd_tag = "TEXT"), │ │ │ │ structure("scale parameter (scalar), and normalized residuals of length\n", Rd_tag = "TEXT"), │ │ │ │ structure("sum(zeroIndices).\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/doZeroMStep.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/doZeroMStep.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ expSummary (list) = structure(list(structure(list(structure("Access MRexperiment object experiment data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("expSummary", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("expSummary", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("expSummary,MRexperiment-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The expSummary vectors represent the column (sample specific) sums of\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1110,15 +1110,15 @@ │ │ │ │ structure(list(structure("MRexperiment", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" object.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Experiment summary table\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Joseph N. Paulson, jpaulson@umiacs.umd.edu\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("expSummary(mouseData)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/expSummary.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/expSummary.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ exportMat (list) = structure(list(structure(list(structure("Export the normalized MRexperiment dataset as a matrix.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("exportMat", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("exportMat", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("exportMatrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function allows the user to take a dataset of counts and output the\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1147,15 +1147,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("cumNorm", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(lungData)\n", Rd_tag = "RCODE"), structure("dataDirectory <- system.file(\"extdata\", package=\"metagenomeSeq\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("exportMat(lungData[,1:5],file=file.path(dataDirectory,\"tmp.tsv\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(read.csv(file=file.path(dataDirectory,\"tmp.tsv\"),sep=\"\\t\"))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/exportMat.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/exportMat.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ exportStats (list) = structure(list(structure(list(structure("Various statistics of the count data.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("exportStats", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("exportStats", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A matrix of values for each sample. The matrix consists of sample ids, the\n", Rd_tag = "TEXT"), │ │ │ │ structure("sample scaling factor, quantile value, the number identified features, and library size (depth of coverage).\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1176,15 +1176,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("quantile", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(lungData)\n", Rd_tag = "RCODE"), structure("dataDirectory <- system.file(\"extdata\", package=\"metagenomeSeq\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("exportStats(lungData[,1:5],file=file.path(dataDirectory,\"tmp.tsv\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(read.csv(file=file.path(dataDirectory,\"tmp.tsv\"),sep=\"\\t\"))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/exportStats.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/exportStats.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extractMR (list) = structure(list(structure(list(structure("Extract the essentials of an MRexperiment.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extractMR", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extractMR", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Extract the essentials of an MRexperiment.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("extractMR(obj)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1197,15 +1197,15 @@ │ │ │ │ structure(list(), Rd_tag = "\\item"), structure(" librarySize : The column sums / library size / sequencing depth \n", Rd_tag = "TEXT"), │ │ │ │ structure(list(), Rd_tag = "\\item"), structure(" normFactors : The normalization scaling factors\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(), Rd_tag = "\\item"), structure(" pheno : phenotype table\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(), Rd_tag = "\\item"), structure(" feat : feature table\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("head(metagenomeSeq:::extractMR(mouseData))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/extractMR.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/extractMR.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ filterData (list) = structure(list(structure(list(structure("Filter datasets according to no. features present in features with at least a certain depth.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("filterData", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("filterData", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Filter the data based on the number of present features after filtering samples by depth of coverage.\n", Rd_tag = "TEXT"), │ │ │ │ structure("There are many ways to filter the object, this is just one way.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1218,15 +1218,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("depth", Rd_tag = "TEXT")), │ │ │ │ list(structure("Sampls with at least this much depth of coverage", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A MRexperiment object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("filterData(mouseData)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/filterData.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/filterData.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fitDO (list) = structure(list(structure(list(structure("Wrapper to calculate Discovery Odds Ratios on feature values.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitDO", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitDO", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function returns a data frame of p-values, odds ratios, lower and upper\n", Rd_tag = "TEXT"), │ │ │ │ structure("confidence limits for every row of a matrix. The discovery odds ratio is calculated\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1271,15 +1271,15 @@ │ │ │ │ structure("fitMeta", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(lungData)\n", Rd_tag = "RCODE"), structure("k = grep(\"Extraction.Control\",pData(lungData)$SampleType)\n", Rd_tag = "RCODE"), │ │ │ │ structure("lungTrim = lungData[,-k]\n", Rd_tag = "RCODE"), │ │ │ │ structure("lungTrim = lungTrim[-which(rowSums(MRcounts(lungTrim)>0)<20),]\n", Rd_tag = "RCODE"), │ │ │ │ structure("res = fitDO(lungTrim,pData(lungTrim)$SmokingStatus);\n", Rd_tag = "RCODE"), │ │ │ │ - structure("head(res)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitDO.Rd", class = "Rd", meta = list( │ │ │ │ + structure("head(res)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/fitDO.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fitFeatureModel (list) = structure(list(structure(list(structure("Computes differential abundance analysis using a zero-inflated log-normal model", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitFeatureModel", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitFeatureModel", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Wrapper to actually run zero-inflated log-normal model given a MRexperiment object\n", Rd_tag = "TEXT"), │ │ │ │ structure("and model matrix. User can decide to shrink parameter estimates.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1333,15 +1333,15 @@ │ │ │ │ structure("data(lungData)\n", Rd_tag = "RCODE"), structure("lungData = lungData[,-which(is.na(pData(lungData)$SmokingStatus))]\n", Rd_tag = "RCODE"), │ │ │ │ structure("lungData=filterData(lungData,present=30,depth=1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("lungData <- cumNorm(lungData, p=.5)\n", Rd_tag = "RCODE"), │ │ │ │ structure("s <- normFactors(lungData)\n", Rd_tag = "RCODE"), │ │ │ │ structure("pd <- pData(lungData)\n", Rd_tag = "RCODE"), │ │ │ │ structure("mod <- model.matrix(~1+SmokingStatus, data=pd)\n", Rd_tag = "RCODE"), │ │ │ │ structure("lungres1 = fitFeatureModel(lungData,mod)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitFeatureModel.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/fitFeatureModel.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fitFeatureModelResults-class (list) = structure(list(structure(list(structure("Class \"fitFeatureModelResults\" -- a formal class for storing results from a fitFeatureModel call", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitFeatureModelResults-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitFeatureModelResults-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This class contains all of the same information expected from a fitFeatureModel call, \n", Rd_tag = "TEXT"), │ │ │ │ structure("but it is defined in the S4 style as opposed to being stored as a list.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1364,15 +1364,15 @@ │ │ │ │ list(structure("count matrix", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure(list(structure("pvalues", Rd_tag = "RCODE")), Rd_tag = "\\code")), │ │ │ │ list(structure("calculated p-values", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure(list(structure("permuttedFits", Rd_tag = "RCODE")), Rd_tag = "\\code")), │ │ │ │ list(structure("permutted z-score estimates under the null", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\describe"))), Rd_tag = "\\section")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitFeatureModelResults-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\describe"))), Rd_tag = "\\section")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/fitFeatureModelResults-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fitLogNormal (list) = structure(list(structure(list(structure("Computes a log-normal linear model and permutation based p-values.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitLogNormal", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitLogNormal", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Wrapper to perform the permutation test on the t-statistic. This is the original\n", Rd_tag = "TEXT"), │ │ │ │ structure("method employed by metastats (for non-sparse large samples). We include CSS normalization\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1404,15 +1404,15 @@ │ │ │ │ structure("lungTrim = lungData[,-k]\n", Rd_tag = "RCODE"), │ │ │ │ structure("k = which(rowSums(MRcounts(lungTrim)>0)<30)\n", Rd_tag = "RCODE"), │ │ │ │ structure("lungTrim = cumNorm(lungTrim)\n", Rd_tag = "RCODE"), │ │ │ │ structure("lungTrim = lungTrim[-k,]\n", Rd_tag = "RCODE"), │ │ │ │ structure("smokingStatus = pData(lungTrim)$SmokingStatus\n", Rd_tag = "RCODE"), │ │ │ │ structure("mod = model.matrix(~smokingStatus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("fit = fitLogNormal(obj = lungTrim,mod=mod,B=1)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitLogNormal.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/fitLogNormal.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fitMultipleTimeSeries (list) = structure(list(structure(list(structure("Discover differentially abundant time intervals for all bacteria", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitMultipleTimeSeries", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitMultipleTimeSeries", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate time intervals of significant differential abundance over all\n", Rd_tag = "TEXT"), │ │ │ │ structure("bacteria of a particularly specified level (lvl). If not lvl is specified,\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1460,15 +1460,15 @@ │ │ │ │ structure("fitSSTimeSeries", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("fitTimeSeries", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("res = fitMultipleTimeSeries(obj=mouseData,lvl='phylum',class=\"status\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" id=\"mouseID\",time=\"relativeTime\",B=1)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitMultipleTimeSeries.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/fitMultipleTimeSeries.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fitPA (list) = structure(list(structure(list(structure("Wrapper to run fisher's test on presence/absence of a feature.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitPA", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitPA", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function returns a data frame of p-values, odds ratios, lower and upper\n", Rd_tag = "TEXT"), │ │ │ │ structure("confidence limits for every row of a matrix.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1507,15 +1507,15 @@ │ │ │ │ structure("fitMeta", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(lungData)\n", Rd_tag = "RCODE"), structure("k = grep(\"Extraction.Control\",pData(lungData)$SampleType)\n", Rd_tag = "RCODE"), │ │ │ │ structure("lungTrim = lungData[,-k]\n", Rd_tag = "RCODE"), │ │ │ │ structure("lungTrim = lungTrim[-which(rowSums(MRcounts(lungTrim)>0)<20),]\n", Rd_tag = "RCODE"), │ │ │ │ structure("res = fitPA(lungTrim,pData(lungTrim)$SmokingStatus);\n", Rd_tag = "RCODE"), │ │ │ │ - structure("head(res)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitPA.Rd", class = "Rd", meta = list( │ │ │ │ + structure("head(res)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/fitPA.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fitSSTimeSeries (list) = structure(list(structure(list(structure("Discover differentially abundant time intervals using SS-Anova", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitSSTimeSeries", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitSSTimeSeries", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate time intervals of interest using SS-Anova fitted models.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Fitting is performed uses Smoothing Spline ANOVA (SS-Anova) to find interesting intervals of time. \n", Rd_tag = "TEXT"), │ │ │ │ @@ -1611,15 +1611,15 @@ │ │ │ │ structure("ssPermAnalysis", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("plotTimeSeries", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("res = fitSSTimeSeries(obj=mouseData,feature=\"Actinobacteria\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" class=\"status\",id=\"mouseID\",time=\"relativeTime\",lvl='class',B=2)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitSSTimeSeries.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/fitSSTimeSeries.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fitTimeSeries (list) = structure(list(structure(list(structure("Discover differentially abundant time intervals", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitTimeSeries", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitTimeSeries", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate time intervals of significant differential abundance.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Currently only one method is implemented (ssanova). fitSSTimeSeries is called with method=\"ssanova\".\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1706,15 +1706,15 @@ │ │ │ │ structure("fitSSTimeSeries", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("plotTimeSeries", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("res = fitTimeSeries(obj=mouseData,feature=\"Actinobacteria\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" class=\"status\",id=\"mouseID\",time=\"relativeTime\",lvl='class',B=2)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitTimeSeries.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/fitTimeSeries.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fitZeroLogNormal (list) = structure(list(structure(list(structure("Compute the log fold-change estimates for the zero-inflated log-normal model", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitZeroLogNormal", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitZeroLogNormal", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Run the zero-inflated log-normal model given a MRexperiment object\n", Rd_tag = "TEXT"), │ │ │ │ structure("and model matrix. Not for the average user, assumes structure of the model matrix.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1770,15 +1770,15 @@ │ │ │ │ structure("zeroExclude - features to exclude for various reasons, e.g. all zeros", Rd_tag = "TEXT")), Rd_tag = "LIST"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("cumNorm", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("fitFeatureModel", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitZeroLogNormal.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/fitZeroLogNormal.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fitZig (list) = structure(list(structure(list(structure("Computes the weighted fold-change estimates and t-statistics.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitZig", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitZig", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Wrapper to actually run the Expectation-maximization algorithm and estimate\n", Rd_tag = "TEXT"), │ │ │ │ structure("$f_count$ fits. Maximum-likelihood estimates are approximated using the EM\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1871,15 +1871,15 @@ │ │ │ │ structure("lungTrim = cumNorm(lungTrim)\n", Rd_tag = "RCODE"), │ │ │ │ structure("lungTrim = lungTrim[-k,]\n", Rd_tag = "RCODE"), │ │ │ │ structure("smokingStatus = pData(lungTrim)$SmokingStatus\n", Rd_tag = "RCODE"), │ │ │ │ structure("mod = model.matrix(~smokingStatus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# The maxit is not meant to be 1 - this is for demonstration/speed\n", Rd_tag = "RCODE"), │ │ │ │ structure("settings = zigControl(maxit=1,verbose=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("fit = fitZig(obj = lungTrim,mod=mod,control=settings)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitZig.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/fitZig.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fitZigResults-class (list) = structure(list(structure(list(structure("Class \"fitZigResults\" -- a formal class for storing results from a fitZig call", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitZigResults-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitZigResults-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This class contains all of the same information expected from a fitZig call, \n", Rd_tag = "TEXT"), │ │ │ │ structure("but it is defined in the S4 style as opposed to being stored as a list.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1921,15 +1921,15 @@ │ │ │ │ list(structure("convergence", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure(list(structure("stillActiveNLL", Rd_tag = "RCODE")), Rd_tag = "\\code")), │ │ │ │ list(structure("nll at convergence", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure(list(structure("dupcor", Rd_tag = "RCODE")), Rd_tag = "\\code")), │ │ │ │ list(structure("correlation of duplicates", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\describe"))), Rd_tag = "\\section")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitZigResults-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\describe"))), Rd_tag = "\\section")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/fitZigResults-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getCountDensity (list) = structure(list(structure(list(structure("Compute the value of the count density function from the count model\n", Rd_tag = "TEXT"), │ │ │ │ structure("residuals.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getCountDensity", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getCountDensity", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate density values from a normal: $f(x) = 1/(sqrt (2 pi ) sigma )\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1947,15 +1947,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("log", Rd_tag = "TEXT")), │ │ │ │ list(structure("Whether or not we are calculating from a log-normal distribution.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Density values from the count model residuals.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/getCountDensity.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/getCountDensity.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getEpsilon (list) = structure(list(structure(list(structure("Calculate the relative difference between iterations of the negative\n", Rd_tag = "TEXT"), │ │ │ │ structure("log-likelihoods.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getEpsilon", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getEpsilon", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Maximum-likelihood estimates are approximated using the EM algorithm where\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1972,15 +1972,15 @@ │ │ │ │ list(structure("Vector of size M with the previous iterations negative\n", Rd_tag = "TEXT"), │ │ │ │ structure("log-likelihoods.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Vector of size M of the relative differences between the previous\n", Rd_tag = "TEXT"), │ │ │ │ structure("and current iteration nll.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/getEpsilon.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/getEpsilon.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getNegativeLogLikelihoods (list) = structure(list(structure(list(structure("Calculate the negative log-likelihoods for the various features given the\n", Rd_tag = "TEXT"), │ │ │ │ structure("residuals.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getNegativeLogLikelihoods", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getNegativeLogLikelihoods", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Maximum-likelihood estimates are approximated using the EM algorithm where\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2000,15 +2000,15 @@ │ │ │ │ structure(list(list(structure("zeroResiduals", Rd_tag = "TEXT")), │ │ │ │ list(structure("Residuals from the zero model.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Vector of size M of the negative log-likelihoods for the various\n", Rd_tag = "TEXT"), │ │ │ │ structure("features.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/getNegativeLogLikelihoods.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/getNegativeLogLikelihoods.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getPi (list) = structure(list(structure(list(structure("Calculate the mixture proportions from the zero model / spike mass model\n", Rd_tag = "TEXT"), │ │ │ │ structure("residuals.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getPi", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getPi", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("F(x) = 1 / (1 + exp(-(x-m)/s)) (the CDF of the logistic distribution).\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2019,15 +2019,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getPi(residuals)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("residuals", Rd_tag = "TEXT")), list(structure("Residuals from the zero model.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Mixture proportions for each sample.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/getPi.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/getPi.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ getZ (list) = structure(list(structure(list(structure("Calculate the current Z estimate responsibilities (posterior probabilities)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("getZ", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("getZ", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the current Z estimate responsibilities (posterior probabilities)\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("getZ(z, zUsed, stillActive, nll, nllUSED)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2049,15 +2049,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("nllUSED", Rd_tag = "TEXT")), │ │ │ │ list(structure("Vector of size M with the converged negative log-likelihoods.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A list of updated zUsed and nllUSED.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/getZ.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/getZ.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ isItStillActive (list) = structure(list(structure(list(structure("Function to determine if a feature is still active.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("isItStillActive", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("isItStillActive", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -2078,15 +2078,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("nll", Rd_tag = "TEXT")), │ │ │ │ list(structure("Vector of size M with the current negative log-likelihoods.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("None.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/isItStillActive.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/isItStillActive.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ libSize (list) = structure(list(structure(list(structure("Access sample depth of coverage from MRexperiment object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("libSize", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("libSize", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Access the libSize vector represents the column (sample specific) sums of features,\n", Rd_tag = "TEXT"), │ │ │ │ structure("i.e. the total number of reads for a sample or depth of coverage. It is used by\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2098,15 +2098,15 @@ │ │ │ │ structure(list(structure("MRexperiment", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Library sizes\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Joseph N. Paulson\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(lungData)\n", Rd_tag = "RCODE"), structure("head(libSize(lungData))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/libSize.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/libSize.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ libSize-set (list) = structure(list(structure(list(structure("Replace the library sizes in a MRexperiment object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("libSize<-", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("libSize<-", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("libSize<-,MRexperiment,numeric-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Function to replace the scaling factors, aka the library sizes, of\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2122,15 +2122,15 @@ │ │ │ │ structure(list(list(structure("value", Rd_tag = "TEXT")), │ │ │ │ list(structure("vector of library sizes", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("vector library sizes\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Joseph N. Paulson\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(lungData)\n", Rd_tag = "RCODE"), structure("head(libSize(lungData)<- rnorm(1))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/libSize-set.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/libSize-set.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ loadBiom (list) = structure(list(structure(list(structure("Load objects organized in the Biom format.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("loadBiom", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("loadBiom", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Wrapper to load Biom formatted object.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("loadBiom(file)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2147,15 +2147,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("biom2MRexperiment", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("#library(biomformat)\n", Rd_tag = "RCODE"), │ │ │ │ structure("rich_dense_file = system.file(\"extdata\", \"rich_dense_otu_table.biom\", package = \"biomformat\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("x = loadBiom(rich_dense_file)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("x\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/loadBiom.Rd", class = "Rd", meta = list( │ │ │ │ + structure("x\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/loadBiom.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ loadMeta (list) = structure(list(structure(list(structure("Load a count dataset associated with a study.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("loadMeta", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("loadMeta", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("metagenomicLoader", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Load a matrix of OTUs in a tab delimited format\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2169,15 +2169,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A list with objects 'counts' and 'taxa'.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("loadPhenoData", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("dataDirectory <- system.file(\"extdata\", package=\"metagenomeSeq\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("lung = loadMeta(file.path(dataDirectory,\"CHK_NAME.otus.count.csv\"))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/loadMeta.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/loadMeta.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ loadMetaQ (list) = structure(list(structure(list(structure("Load a count dataset associated with a study set up in a Qiime format.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("loadMetaQ", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("loadMetaQ", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("qiimeLoader", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Load a matrix of OTUs in Qiime's format\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2188,15 +2188,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An list with 'counts' containing the count data, 'taxa' containing the otu annotation, and 'otus'.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("loadMeta", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("loadPhenoData", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# see vignette\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/loadMetaQ.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# see vignette\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/loadMetaQ.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ loadPhenoData (list) = structure(list(structure(list(structure("Load a clinical/phenotypic dataset associated with a study.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("loadPhenoData", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("loadPhenoData", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("phenoData", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Load a matrix of metadata associated with a study.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2214,24 +2214,24 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The metadata as a dataframe.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("loadMeta", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("dataDirectory <- system.file(\"extdata\", package=\"metagenomeSeq\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("clin = loadPhenoData(file.path(dataDirectory,\"CHK_clinical.csv\"),tran=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/loadPhenoData.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/loadPhenoData.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ lungData (list) = structure(list(structure(list(structure("OTU abundance matrix of samples from a smoker/non-smoker study", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("lungData", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("lungData", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("This is a list with a matrix of OTU counts,otu names, taxa annotations for each OTU, and phenotypic data. Samples along the columns and OTUs along the rows.", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("A list of OTU matrix, taxa, otus, and phenotypes", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("MRexperiment-class object of 16S lung samples.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("http://www.ncbi.nlm.nih.gov/pubmed/21680950", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/lungData.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("http://www.ncbi.nlm.nih.gov/pubmed/21680950", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/lungData.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ makeLabels (list) = structure(list(structure(list(structure("Function to make labels simpler", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("makeLabels", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("makeLabels", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Beginning to transition to better axes for plots\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("makeLabels(x = \"samples\", y = \"abundance\", norm, log)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2244,15 +2244,15 @@ │ │ │ │ structure(list(list(structure("norm", Rd_tag = "TEXT")), │ │ │ │ list(structure("is the data normalized?", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("log", Rd_tag = "TEXT")), │ │ │ │ list(structure("is the data logged?", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("vector of x,y labels\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "RCODE"), structure("metagenomeSeq::makeLabels(norm=TRUE,log=TRUE) \n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/makeLabels.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "RCODE"), structure("metagenomeSeq::makeLabels(norm=TRUE,log=TRUE) \n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/makeLabels.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ mergeMRexperiments (list) = structure(list(structure(list(structure("Merge two MRexperiment objects together", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mergeMRexperiments", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mergeMRexperiments", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function will take two MRexperiment objects and merge them together finding common\n", Rd_tag = "TEXT"), │ │ │ │ structure("OTUs. If there are OTUs not found in one of the two MRexperiments then a message will\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2266,29 +2266,29 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Merged MRexperiment-class object.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(mouseData)\n", Rd_tag = "RCODE"), │ │ │ │ structure("newobj = mergeMRexperiments(mouseData,mouseData)\n", Rd_tag = "RCODE"), │ │ │ │ structure("newobj\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("# let me know if people are interested in an option to merge by keys instead of row names.\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(lungData)\n", Rd_tag = "RCODE"), structure("newobj = mergeMRexperiments(mouseData,lungData)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("newobj\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/mergeMRexperiments.Rd", class = "Rd", meta = list( │ │ │ │ + structure("newobj\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/mergeMRexperiments.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ mergeTable (list) = structure(list(structure(list(structure("Merge two tables", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mergeTable", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mergeTable", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Merge two tables\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mergeTable(x, y)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("x", Rd_tag = "TEXT")), list(structure("Table 1.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("y", Rd_tag = "TEXT")), │ │ │ │ list(structure("Table 2.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("Merged table\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/mergeTable.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("Merged table\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/mergeTable.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ metagenomeSeq-deprecated (list) = structure(list(structure(list(structure("Depcrecated functions in the metagenomeSeq package.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("metagenomeSeq-deprecated", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("metagenomeSeq-deprecated", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("deprecated_metagenomeSeq_function", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("fitMeta", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -2305,38 +2305,38 @@ │ │ │ │ structure(list(list(structure("value", Rd_tag = "TEXT")), │ │ │ │ list(structure("For assignment operators, the value to replace with \n", Rd_tag = "TEXT"), │ │ │ │ structure("(the right side of the assignment).", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("...", Rd_tag = "TEXT")), │ │ │ │ list(structure("For functions other than assignment operators, \n", Rd_tag = "TEXT"), │ │ │ │ structure("parameters to be passed to the modern version of the function (see table).", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/metagenomeSeq-deprecated.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/metagenomeSeq-deprecated.Rd", class = "Rd", meta = list( │ │ │ │ docType = "package", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ metagenomeSeq-package (list) = structure(list(structure(list(structure("Statistical analysis for sparse high-throughput sequencing", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("metagenomeSeq-package", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("metagenomeSeq", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("metagenomeSeq-package", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("package", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("A user's guide is available, and can be opened by typing ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("vignette(\"metagenomeSeq\")", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" \n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("The metagenomeSeq package implements novel normalization and statistical methodology in the following papers.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Paulson, JN ; Pop, M; Corrada Bravo, H\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("Paulson, Joseph N., O. Colin Stine, Hector Corrada Bravo, and Mihai Pop. \"Differential abundance analysis for microbial marker-gene surveys.\" Nature methods (2013).\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/metagenomeSeq-package.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("Paulson, Joseph N., O. Colin Stine, Hector Corrada Bravo, and Mihai Pop. \"Differential abundance analysis for microbial marker-gene surveys.\" Nature methods (2013).\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/metagenomeSeq-package.Rd", class = "Rd", meta = list( │ │ │ │ docType = "package", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ mouseData (list) = structure(list(structure(list(structure("OTU abundance matrix of mice samples from a diet longitudinal study", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mouseData", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mouseData", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("This is a list with a matrix of OTU counts, taxa annotations for each OTU, otu names, and vector of phenotypic data. Samples along the columns and OTUs along the rows.", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("A list of OTU matrix, taxa, otus, and phenotypes", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("MRexperiment-class object of 16S mouse samples.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894525/", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/mouseData.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894525/", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/mouseData.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ newMRexperiment (list) = structure(list(structure(list(structure("Create a MRexperiment object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("newMRexperiment", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("newMRexperiment", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function creates a MRexperiment object from a matrix or data frame of\n", Rd_tag = "TEXT"), │ │ │ │ structure("count data.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2370,15 +2370,15 @@ │ │ │ │ structure(" and ", Rd_tag = "TEXT"), structure(list(structure("eSet", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" (from the Biobase\n", Rd_tag = "TEXT"), structure("package) for the meaning of the various slots.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("an object of class MRexperiment\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Joseph N Paulson\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("cnts = matrix(abs(rnorm(1000)),nc=10)\n", Rd_tag = "RCODE"), │ │ │ │ structure("obj <- newMRexperiment(cnts)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/newMRexperiment.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/newMRexperiment.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ normFactors (list) = structure(list(structure(list(structure("Access the normalization factors in a MRexperiment object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("normFactors", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("normFactors", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Function to access the scaling factors, aka the normalization factors, of\n", Rd_tag = "TEXT"), │ │ │ │ structure("samples in a MRexperiment object.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2388,15 +2388,15 @@ │ │ │ │ structure(list(structure("MRexperiment", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Normalization scaling factors\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Joseph N. Paulson\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(lungData)\n", Rd_tag = "RCODE"), structure("head(normFactors(lungData))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/normFactors.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/normFactors.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ normFactors-set (list) = structure(list(structure(list(structure("Replace the normalization factors in a MRexperiment object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("normFactors<-", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("normFactors<-", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("normFactors<-,MRexperiment,numeric-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Function to replace the scaling factors, aka the normalization factors, of\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2413,15 +2413,15 @@ │ │ │ │ structure(list(list(structure("value", Rd_tag = "TEXT")), │ │ │ │ list(structure("vector of normalization scaling factors", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Normalization scaling factors\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Joseph N. Paulson\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(lungData)\n", Rd_tag = "RCODE"), structure("head(normFactors(lungData)<- rnorm(1))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/normFactors-set.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/normFactors-set.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotBubble (list) = structure(list(structure(list(structure("Basic plot of binned vectors.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotBubble", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotBubble", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function plots takes two vectors, calculates the contingency table and \n", Rd_tag = "TEXT"), │ │ │ │ structure("plots circles sized by the contingency table value. Optional significance vectors\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2467,15 +2467,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("mouseData = mouseData[which(rowSums(mouseData)>139),]\n", Rd_tag = "RCODE"), │ │ │ │ structure("sparsity = rowMeans(MRcounts(mouseData)==0)\n", Rd_tag = "RCODE"), │ │ │ │ structure("lor = log(fitPA(mouseData,cl=pData(mouseData)[,3])$oddsRatio)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotBubble(lor,sparsity,main=\"lor ~ sparsity\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Example 2\n", Rd_tag = "RCODE"), structure("x = runif(100000)\n", Rd_tag = "RCODE"), │ │ │ │ structure("y = runif(100000)\n", Rd_tag = "RCODE"), structure("plotBubble(y,x)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotBubble.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/plotBubble.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotClassTimeSeries (list) = structure(list(structure(list(structure("Plot abundances by class", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotClassTimeSeries", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotClassTimeSeries", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot the abundance of values for each class using \n", Rd_tag = "TEXT"), │ │ │ │ structure("a spline approach on the estimated full model.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2515,15 +2515,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitTimeSeries", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("res = fitTimeSeries(obj=mouseData,feature=\"Actinobacteria\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" class=\"status\",id=\"mouseID\",time=\"relativeTime\",lvl='class',B=10)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotClassTimeSeries(res,pch=21,bg=res$data$class,ylim=c(0,8))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotClassTimeSeries.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/plotClassTimeSeries.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotCorr (list) = structure(list(structure(list(structure("Basic correlation plot function for normalized or unnormalized counts.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotCorr", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotCorr", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function plots a heatmap of the \"n\" features with greatest variance\n", Rd_tag = "TEXT"), │ │ │ │ structure("across rows.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2550,15 +2550,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("plotted correlation matrix\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("cumNormMat", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("plotCorr(obj=mouseData,n=200,cexRow = 0.4,cexCol = 0.4,trace=\"none\",dendrogram=\"none\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" col = colorRampPalette(brewer.pal(9, \"RdBu\"))(50))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotCorr.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/plotCorr.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotFeature (list) = structure(list(structure(list(structure("Basic plot function of the raw or normalized data.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotFeature", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotFeature", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function plots the abundance of a particular OTU by class. The function\n", Rd_tag = "TEXT"), │ │ │ │ structure("is the typical manhattan plot of the abundances.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2606,15 +2606,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("classIndex=list(Western=which(pData(mouseData)$diet==\"Western\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("classIndex$BK=which(pData(mouseData)$diet==\"BK\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("otuIndex = 8770\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("par(mfrow=c(2,1))\n", Rd_tag = "RCODE"), structure("dates = pData(mouseData)$date\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotFeature(mouseData,norm=FALSE,log=FALSE,otuIndex,classIndex,\n", Rd_tag = "RCODE"), │ │ │ │ structure("col=dates,sortby=dates,ylab=\"Raw reads\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotFeature.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/plotFeature.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotGenus (list) = structure(list(structure(list(structure("Basic plot function of the raw or normalized data.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotGenus", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotGenus", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("genusPlot", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function plots the abundance of a particular OTU by class. The function\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2674,15 +2674,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("classIndex=list(controls=which(pData(mouseData)$diet==\"BK\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("classIndex$cases=which(pData(mouseData)$diet==\"Western\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("otuIndex = grep(\"Strep\",fData(mouseData)$family)\n", Rd_tag = "RCODE"), │ │ │ │ structure("otuIndex=otuIndex[order(rowSums(MRcounts(mouseData)[otuIndex,]),decreasing=TRUE)]\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotGenus(mouseData,otuIndex,classIndex,no=1:2,xaxt=\"n\",norm=FALSE,ylab=\"Strep normalized log(cpt)\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotGenus.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/plotGenus.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotMRheatmap (list) = structure(list(structure(list(structure("Basic heatmap plot function for normalized counts.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotMRheatmap", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotMRheatmap", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function plots a heatmap of the 'n' features with greatest variance\n", Rd_tag = "TEXT"), │ │ │ │ structure("across rows (or other statistic).\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2715,15 +2715,15 @@ │ │ │ │ structure("heatmapCols = colorRampPalette(brewer.pal(9, \"RdBu\"))(50)\n", Rd_tag = "RCODE"), │ │ │ │ structure("#### version using sd\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotMRheatmap(obj=mouseData,n=200,cexRow = 0.4,cexCol = 0.4,trace=\"none\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" col = heatmapCols,ColSideColors = heatmapColColors)\n", Rd_tag = "RCODE"), │ │ │ │ structure("#### version using MAD\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotMRheatmap(obj=mouseData,n=50,fun=mad,cexRow = 0.4,cexCol = 0.4,trace=\"none\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" col = heatmapCols,ColSideColors = heatmapColColors) \n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotMRheatmap.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/plotMRheatmap.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotOTU (list) = structure(list(structure(list(structure("Basic plot function of the raw or normalized data.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotOTU", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotOTU", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function plots the abundance of a particular OTU by class. The function\n", Rd_tag = "TEXT"), │ │ │ │ structure("uses the estimated posterior probabilities to make technical zeros\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2777,15 +2777,15 @@ │ │ │ │ structure(list(structure("cumNorm", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("classIndex=list(controls=which(pData(mouseData)$diet==\"BK\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("classIndex$cases=which(pData(mouseData)$diet==\"Western\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# you can specify whether or not to normalize, and to what level\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotOTU(mouseData,otu=9083,classIndex,norm=FALSE,main=\"9083 feature abundances\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotOTU.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/plotOTU.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotOrd (list) = structure(list(structure(list(structure("Plot of either PCA or MDS coordinates for the distances of normalized or unnormalized counts.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotOrd", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotOrd", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function plots the PCA / MDS coordinates for the \"n\" features of interest. Potentially uncovering batch\n", Rd_tag = "TEXT"), │ │ │ │ structure("effects or feature relationships.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2834,15 +2834,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("coordinates\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("cumNormMat", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("cl = pData(mouseData)[,3]\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotOrd(mouseData,tran=TRUE,useDist=TRUE,pch=21,bg=factor(cl),usePCA=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotOrd.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/plotOrd.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotRare (list) = structure(list(structure(list(structure("Plot of rarefaction effect", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotRare", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotRare", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function plots the number of observed features vs. the depth of coverage.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("plotRare(obj, cl = NULL, ...)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2870,15 +2870,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("cl = factor(pData(mouseData)[,3])\n", Rd_tag = "RCODE"), │ │ │ │ structure("res = plotRare(mouseData,cl=cl,pch=21,bg=cl)\n", Rd_tag = "RCODE"), │ │ │ │ structure("tmp=lapply(levels(cl), function(lv) lm(res[,\"ident\"]~res[,\"libSize\"]-1, subset=cl==lv))\n", Rd_tag = "RCODE"), │ │ │ │ structure("for(i in 1:length(levels(cl))){\n", Rd_tag = "RCODE"), │ │ │ │ structure(" abline(tmp[[i]], col=i)\n", Rd_tag = "RCODE"), │ │ │ │ structure("}\n", Rd_tag = "RCODE"), structure("legend(\"topleft\", c(\"Diet 1\",\"Diet 2\"), text.col=c(1,2),box.col=NA)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotRare.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/plotRare.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plotTimeSeries (list) = structure(list(structure(list(structure("Plot difference function for particular bacteria", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotTimeSeries", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotTimeSeries", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot the difference in abundance for significant features.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("plotTimeSeries(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -2909,15 +2909,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("fitTimeSeries", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("res = fitTimeSeries(obj=mouseData,feature=\"Actinobacteria\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" class=\"status\",id=\"mouseID\",time=\"relativeTime\",lvl='class',B=10)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotTimeSeries(res)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotTimeSeries.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/plotTimeSeries.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ posteriorProbs (list) = structure(list(structure(list(structure("Access the posterior probabilities that results from analysis", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("posteriorProbs", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("posteriorProbs", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("posteriorProbs,MRexperiment-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Accessing the posterior probabilities following a run through\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2940,15 +2940,15 @@ │ │ │ │ structure("lungTrim = lungTrim[-k,]\n", Rd_tag = "RCODE"), │ │ │ │ structure("smokingStatus = pData(lungTrim)$SmokingStatus\n", Rd_tag = "RCODE"), │ │ │ │ structure("mod = model.matrix(~smokingStatus)\n", Rd_tag = "RCODE"), │ │ │ │ structure("# The maxit is not meant to be 1 -- this is for demonstration/speed\n", Rd_tag = "RCODE"), │ │ │ │ structure("settings = zigControl(maxit=1,verbose=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("fit = fitZig(obj = lungTrim,mod=mod,control=settings)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(posteriorProbs(lungTrim))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/posteriorProbs.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/posteriorProbs.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ returnAppropriateObj (list) = structure(list(structure(list(structure("Check if MRexperiment or matrix and return matrix", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("returnAppropriateObj", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("returnAppropriateObj", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Function to check if object is a MRexperiment\n", Rd_tag = "TEXT"), │ │ │ │ structure("class or matrix\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2972,15 +2972,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("sl", Rd_tag = "TEXT")), │ │ │ │ list(structure("scaling value", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Matrix\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(lungData)\n", Rd_tag = "RCODE"), structure("head(returnAppropriateObj(lungData,norm=FALSE,log=FALSE))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/returnAppropriateObj.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/returnAppropriateObj.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -3039,15 +3039,15 @@ │ │ │ │ structure("ssPermAnalysis", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("ssPerm", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("ssIntervalCandidate", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# Not run\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/ssFit.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# Not run\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/ssFit.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ ssIntervalCandidate (list) = structure(list(structure(list(structure("calculate interesting time intervals", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("ssIntervalCandidate", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("ssIntervalCandidate", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculates time intervals of interest using SS-Anova fitted confidence intervals.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("ssIntervalCandidate(fit, standardError, timePoints, positive = TRUE, C = 0)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -3075,15 +3075,15 @@ │ │ │ │ structure("ssFit", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("ssPerm", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("ssPermAnalysis", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# Not run\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/ssIntervalCandidate.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# Not run\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/ssIntervalCandidate.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ ssPerm (list) = structure(list(structure(list(structure("class permutations for smoothing-spline time series analysis", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("ssPerm", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("ssPerm", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Creates a list of permuted class memberships for the time series permuation tests.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("ssPerm(df, B)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -3102,15 +3102,15 @@ │ │ │ │ structure("ssFit", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("ssPermAnalysis", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("ssIntervalCandidate", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# Not run\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/ssPerm.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# Not run\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/ssPerm.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ ssPermAnalysis (list) = structure(list(structure(list(structure("smoothing-splines anova fits for each permutation", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("ssPermAnalysis", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("ssPermAnalysis", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculates the fit for each permutation and estimates \n", Rd_tag = "TEXT"), │ │ │ │ structure("the area under the null (permutted) model for interesting time \n", Rd_tag = "TEXT"), │ │ │ │ @@ -3150,15 +3150,15 @@ │ │ │ │ structure("ssFit", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("ssPerm", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("ssIntervalCandidate", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# Not run\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/ssPermAnalysis.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# Not run\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/ssPermAnalysis.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ trapz (list) = structure(list(structure(list(structure("Trapezoidal Integration", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("trapz", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("trapz", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Compute the area of a function with values 'y' at the points 'x'.\n", Rd_tag = "TEXT"), │ │ │ │ structure("Function comes from the pracma package.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -3176,15 +3176,15 @@ │ │ │ │ structure(" n <- 101\n", Rd_tag = "RCODE"), structure(" x <- seq(0, pi, len = n)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" y <- sin(x)\n", Rd_tag = "RCODE"), structure(" trapz(x, y) #=> 1.999835504\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Use a correction term at the boundary: -h^2/12*(f'(b)-f'(a))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" h <- x[2] - x[1]\n", Rd_tag = "RCODE"), │ │ │ │ structure(" ca <- (y[2]-y[1]) / h\n", Rd_tag = "RCODE"), │ │ │ │ structure(" cb <- (y[n]-y[n-1]) / h\n", Rd_tag = "RCODE"), │ │ │ │ structure(" trapz(x, y) - h^2/12 * (cb - ca) #=> 1.999999969\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/trapz.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/trapz.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ ts2MRexperiment (list) = structure(list(structure(list(structure("With a list of fitTimeSeries results, generate\n", Rd_tag = "TEXT"), │ │ │ │ structure("an MRexperiment that can be plotted with metavizr", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("ts2MRexperiment", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("ts2MRexperiment", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("With a list of fitTimeSeries results, generate\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3228,15 +3228,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("fitMultipleTimeSeries", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("res = fitMultipleTimeSeries(obj=mouseData,lvl='phylum',class=\"status\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" id=\"mouseID\",time=\"relativeTime\",B=1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("obj = ts2MRexperiment(res)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("obj\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/ts2MRexperiment.Rd", class = "Rd", meta = list( │ │ │ │ + structure("obj\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/ts2MRexperiment.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ uniqueFeatures (list) = structure(list(structure(list(structure("Table of features unique to a group", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("uniqueFeatures", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("uniqueFeatures", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Creates a table of features, their index, number of positive samples in a group,\n", Rd_tag = "TEXT"), │ │ │ │ structure("and the number of reads in a group. Can threshold features by a minimum no. of reads\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3253,15 +3253,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("nreads", Rd_tag = "TEXT")), │ │ │ │ list(structure("The minimum number of raw reads.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Table of features unique to a group\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(mouseData)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(uniqueFeatures(mouseData[1:100,],cl=pData(mouseData)[,3]))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/uniqueFeatures.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/uniqueFeatures.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ wrenchNorm (list) = structure(list(structure(list(structure("Computes normalization factors using wrench instead of cumNorm", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("wrenchNorm", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("wrenchNorm", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculates normalization factors using method published by\n", Rd_tag = "TEXT"), │ │ │ │ structure("M. Sentil Kumar et al. (2018) to compute normalization factors which \n", Rd_tag = "TEXT"), │ │ │ │ @@ -3282,15 +3282,15 @@ │ │ │ │ structure(list(structure("cumNorm", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("data(mouseData)\n", Rd_tag = "RCODE"), structure("mouseData <- wrenchNorm(mouseData, condition = mouseData$diet)\n", Rd_tag = "RCODE"), │ │ │ │ structure("head(normFactors(mouseData))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/wrenchNorm.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/wrenchNorm.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ zigControl (list) = structure(list(structure(list(structure("Settings for the fitZig function", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("zigControl", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("zigControl", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("settings2", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Settings for the fitZig function\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -3322,10 +3322,10 @@ │ │ │ │ structure(list(structure("fitZig", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("cumNorm", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("plotOTU", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("control = zigControl(tol=1e-10,maxit=10,verbose=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-metagenomeseq/man/zigControl.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-metagenomeseq-1.54.0/man/zigControl.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/metagenomeSeq/help/metagenomeSeq.rdx │ │ │ ├── metagenomeSeq.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,529 +1,529 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$MRcoefs │ │ │ │ │ -[1] 280 3343 │ │ │ │ │ +[1] 287 3355 │ │ │ │ │ │ │ │ │ │ $variables$MRcounts │ │ │ │ │ -[1] 3902 1394 │ │ │ │ │ +[1] 3929 1404 │ │ │ │ │ │ │ │ │ │ $variables$`MRexperiment-class` │ │ │ │ │ -[1] 5579 3683 │ │ │ │ │ +[1] 5626 3694 │ │ │ │ │ │ │ │ │ │ $variables$MRexperiment2biom │ │ │ │ │ -[1] 9547 1585 │ │ │ │ │ +[1] 9614 1598 │ │ │ │ │ │ │ │ │ │ $variables$MRfulltable │ │ │ │ │ -[1] 11415 3351 │ │ │ │ │ +[1] 11501 3362 │ │ │ │ │ │ │ │ │ │ $variables$`MRihw-fitFeatureModelResults` │ │ │ │ │ -[1] 15059 1405 │ │ │ │ │ +[1] 15165 1417 │ │ │ │ │ │ │ │ │ │ $variables$`MRihw-fitZigResults` │ │ │ │ │ -[1] 16752 1403 │ │ │ │ │ +[1] 16879 1415 │ │ │ │ │ │ │ │ │ │ $variables$MRihw │ │ │ │ │ -[1] 18433 809 │ │ │ │ │ +[1] 18580 821 │ │ │ │ │ │ │ │ │ │ $variables$MRtable │ │ │ │ │ -[1] 19520 3295 │ │ │ │ │ +[1] 19687 3305 │ │ │ │ │ │ │ │ │ │ $variables$aggregateBySample │ │ │ │ │ -[1] 23099 1471 │ │ │ │ │ +[1] 23285 1482 │ │ │ │ │ │ │ │ │ │ $variables$aggregateByTaxonomy │ │ │ │ │ -[1] 24856 2270 │ │ │ │ │ +[1] 25063 2281 │ │ │ │ │ │ │ │ │ │ $variables$biom2MRexperiment │ │ │ │ │ -[1] 27411 1162 │ │ │ │ │ +[1] 27638 1173 │ │ │ │ │ │ │ │ │ │ $variables$calcNormFactors │ │ │ │ │ -[1] 28855 1167 │ │ │ │ │ +[1] 29102 1179 │ │ │ │ │ │ │ │ │ │ $variables$calcPosComponent │ │ │ │ │ -[1] 30305 996 │ │ │ │ │ +[1] 30573 1008 │ │ │ │ │ │ │ │ │ │ $variables$calcShrinkParameters │ │ │ │ │ -[1] 31587 1166 │ │ │ │ │ +[1] 31875 1178 │ │ │ │ │ │ │ │ │ │ $variables$calcStandardError │ │ │ │ │ -[1] 33036 1303 │ │ │ │ │ +[1] 33346 1316 │ │ │ │ │ │ │ │ │ │ $variables$calcZeroAdjustment │ │ │ │ │ -[1] 34624 1302 │ │ │ │ │ +[1] 34956 1314 │ │ │ │ │ │ │ │ │ │ $variables$calcZeroComponent │ │ │ │ │ -[1] 36210 1000 │ │ │ │ │ +[1] 36563 1012 │ │ │ │ │ │ │ │ │ │ $variables$calculateEffectiveSamples │ │ │ │ │ -[1] 37499 1119 │ │ │ │ │ +[1] 37872 1130 │ │ │ │ │ │ │ │ │ │ $variables$correctIndices │ │ │ │ │ -[1] 38899 1363 │ │ │ │ │ +[1] 39292 1374 │ │ │ │ │ │ │ │ │ │ $variables$correlationTest │ │ │ │ │ -[1] 40544 2458 │ │ │ │ │ +[1] 40957 2471 │ │ │ │ │ │ │ │ │ │ $variables$cumNorm │ │ │ │ │ -[1] 43280 1191 │ │ │ │ │ +[1] 43713 1203 │ │ │ │ │ │ │ │ │ │ $variables$cumNormMat │ │ │ │ │ -[1] 44753 1248 │ │ │ │ │ +[1] 45204 1259 │ │ │ │ │ │ │ │ │ │ $variables$cumNormStat │ │ │ │ │ -[1] 46282 1679 │ │ │ │ │ +[1] 46751 1689 │ │ │ │ │ │ │ │ │ │ $variables$cumNormStatFast │ │ │ │ │ -[1] 48245 1536 │ │ │ │ │ +[1] 48731 1545 │ │ │ │ │ │ │ │ │ │ $variables$doCountMStep │ │ │ │ │ -[1] 50064 1906 │ │ │ │ │ +[1] 50565 1916 │ │ │ │ │ │ │ │ │ │ $variables$doEStep │ │ │ │ │ -[1] 52247 1558 │ │ │ │ │ +[1] 52766 1567 │ │ │ │ │ │ │ │ │ │ $variables$doZeroMStep │ │ │ │ │ -[1] 54088 1740 │ │ │ │ │ +[1] 54622 1752 │ │ │ │ │ │ │ │ │ │ $variables$expSummary │ │ │ │ │ -[1] 56109 1118 │ │ │ │ │ +[1] 56661 1130 │ │ │ │ │ │ │ │ │ │ $variables$exportMat │ │ │ │ │ -[1] 57507 1591 │ │ │ │ │ +[1] 58079 1601 │ │ │ │ │ │ │ │ │ │ $variables$exportStats │ │ │ │ │ -[1] 59378 1439 │ │ │ │ │ +[1] 59968 1449 │ │ │ │ │ │ │ │ │ │ $variables$extractMR │ │ │ │ │ -[1] 61097 1097 │ │ │ │ │ +[1] 61705 1108 │ │ │ │ │ │ │ │ │ │ $variables$filterData │ │ │ │ │ -[1] 62474 1135 │ │ │ │ │ +[1] 63100 1146 │ │ │ │ │ │ │ │ │ │ $variables$fitDO │ │ │ │ │ -[1] 63886 2245 │ │ │ │ │ +[1] 64531 2257 │ │ │ │ │ │ │ │ │ │ $variables$fitFeatureModel │ │ │ │ │ -[1] 66415 2255 │ │ │ │ │ +[1] 67079 2268 │ │ │ │ │ │ │ │ │ │ $variables$`fitFeatureModelResults-class` │ │ │ │ │ -[1] 68961 1366 │ │ │ │ │ +[1] 69646 1378 │ │ │ │ │ │ │ │ │ │ $variables$fitLogNormal │ │ │ │ │ -[1] 70609 1823 │ │ │ │ │ +[1] 71314 1834 │ │ │ │ │ │ │ │ │ │ $variables$fitMultipleTimeSeries │ │ │ │ │ -[1] 72719 2319 │ │ │ │ │ +[1] 73444 2331 │ │ │ │ │ │ │ │ │ │ $variables$fitPA │ │ │ │ │ -[1] 75315 1997 │ │ │ │ │ +[1] 76060 2008 │ │ │ │ │ │ │ │ │ │ $variables$fitSSTimeSeries │ │ │ │ │ -[1] 77594 3717 │ │ │ │ │ +[1] 78359 3729 │ │ │ │ │ │ │ │ │ │ $variables$fitTimeSeries │ │ │ │ │ -[1] 81592 3328 │ │ │ │ │ +[1] 82377 3337 │ │ │ │ │ │ │ │ │ │ $variables$fitZeroLogNormal │ │ │ │ │ -[1] 85205 2133 │ │ │ │ │ +[1] 86008 2147 │ │ │ │ │ │ │ │ │ │ $variables$fitZig │ │ │ │ │ -[1] 87616 3528 │ │ │ │ │ +[1] 88440 3541 │ │ │ │ │ │ │ │ │ │ $variables$`fitZigResults-class` │ │ │ │ │ -[1] 91429 1975 │ │ │ │ │ +[1] 92274 1988 │ │ │ │ │ │ │ │ │ │ $variables$getCountDensity │ │ │ │ │ -[1] 93687 1444 │ │ │ │ │ +[1] 94555 1456 │ │ │ │ │ │ │ │ │ │ $variables$getEpsilon │ │ │ │ │ -[1] 95411 1324 │ │ │ │ │ +[1] 96298 1337 │ │ │ │ │ │ │ │ │ │ $variables$getNegativeLogLikelihoods │ │ │ │ │ -[1] 97026 1436 │ │ │ │ │ +[1] 97934 1447 │ │ │ │ │ │ │ │ │ │ $variables$getPi │ │ │ │ │ -[1] 98738 1079 │ │ │ │ │ +[1] 99665 1092 │ │ │ │ │ │ │ │ │ │ $variables$getZ │ │ │ │ │ -[1] 100093 1345 │ │ │ │ │ +[1] 101042 1356 │ │ │ │ │ │ │ │ │ │ $variables$isItStillActive │ │ │ │ │ -[1] 101721 1396 │ │ │ │ │ +[1] 102690 1406 │ │ │ │ │ │ │ │ │ │ $variables$`libSize-set` │ │ │ │ │ -[1] 103397 1162 │ │ │ │ │ +[1] 104384 1173 │ │ │ │ │ │ │ │ │ │ $variables$libSize │ │ │ │ │ -[1] 104836 1098 │ │ │ │ │ +[1] 105842 1110 │ │ │ │ │ │ │ │ │ │ $variables$loadBiom │ │ │ │ │ -[1] 106211 1168 │ │ │ │ │ +[1] 107238 1177 │ │ │ │ │ │ │ │ │ │ $variables$loadMeta │ │ │ │ │ -[1] 107656 1157 │ │ │ │ │ +[1] 108701 1165 │ │ │ │ │ │ │ │ │ │ $variables$loadMetaQ │ │ │ │ │ -[1] 109092 1078 │ │ │ │ │ +[1] 110153 1089 │ │ │ │ │ │ │ │ │ │ $variables$loadPhenoData │ │ │ │ │ -[1] 110452 1294 │ │ │ │ │ +[1] 111532 1306 │ │ │ │ │ │ │ │ │ │ $variables$lungData │ │ │ │ │ -[1] 112024 773 │ │ │ │ │ +[1] 113124 784 │ │ │ │ │ │ │ │ │ │ $variables$makeLabels │ │ │ │ │ -[1] 113077 1025 │ │ │ │ │ +[1] 114195 1037 │ │ │ │ │ │ │ │ │ │ $variables$mergeMRexperiments │ │ │ │ │ -[1] 114387 1148 │ │ │ │ │ +[1] 115526 1160 │ │ │ │ │ │ │ │ │ │ $variables$mergeTable │ │ │ │ │ -[1] 115815 718 │ │ │ │ │ +[1] 116972 730 │ │ │ │ │ │ │ │ │ │ $variables$`metagenomeSeq-deprecated` │ │ │ │ │ -[1] 116816 1239 │ │ │ │ │ +[1] 117993 1250 │ │ │ │ │ │ │ │ │ │ $variables$`metagenomeSeq-package` │ │ │ │ │ -[1] 118336 1223 │ │ │ │ │ +[1] 119533 1236 │ │ │ │ │ │ │ │ │ │ $variables$mouseData │ │ │ │ │ -[1] 119838 794 │ │ │ │ │ +[1] 121055 804 │ │ │ │ │ │ │ │ │ │ $variables$newMRexperiment │ │ │ │ │ -[1] 120916 1840 │ │ │ │ │ +[1] 122151 1851 │ │ │ │ │ │ │ │ │ │ $variables$`normFactors-set` │ │ │ │ │ -[1] 123038 1164 │ │ │ │ │ +[1] 124293 1176 │ │ │ │ │ │ │ │ │ │ $variables$normFactors │ │ │ │ │ -[1] 124482 967 │ │ │ │ │ +[1] 125757 981 │ │ │ │ │ │ │ │ │ │ $variables$plotBubble │ │ │ │ │ -[1] 125730 2138 │ │ │ │ │ +[1] 127025 2147 │ │ │ │ │ │ │ │ │ │ $variables$plotClassTimeSeries │ │ │ │ │ -[1] 128153 1842 │ │ │ │ │ +[1] 129464 1853 │ │ │ │ │ │ │ │ │ │ $variables$plotCorr │ │ │ │ │ -[1] 130273 1582 │ │ │ │ │ +[1] 131603 1593 │ │ │ │ │ │ │ │ │ │ $variables$plotFeature │ │ │ │ │ -[1] 132137 2124 │ │ │ │ │ +[1] 133484 2130 │ │ │ │ │ │ │ │ │ │ $variables$plotGenus │ │ │ │ │ -[1] 134541 2455 │ │ │ │ │ +[1] 135900 2466 │ │ │ │ │ │ │ │ │ │ $variables$plotMRheatmap │ │ │ │ │ -[1] 137279 1745 │ │ │ │ │ +[1] 138656 1755 │ │ │ │ │ │ │ │ │ │ $variables$plotOTU │ │ │ │ │ -[1] 139303 2238 │ │ │ │ │ +[1] 140697 2248 │ │ │ │ │ │ │ │ │ │ $variables$plotOrd │ │ │ │ │ -[1] 141818 2104 │ │ │ │ │ +[1] 143230 2112 │ │ │ │ │ │ │ │ │ │ $variables$plotRare │ │ │ │ │ -[1] 144201 1637 │ │ │ │ │ +[1] 145628 1646 │ │ │ │ │ │ │ │ │ │ $variables$plotTimeSeries │ │ │ │ │ -[1] 146120 1537 │ │ │ │ │ +[1] 147563 1548 │ │ │ │ │ │ │ │ │ │ $variables$posteriorProbs │ │ │ │ │ -[1] 147939 1459 │ │ │ │ │ +[1] 149401 1472 │ │ │ │ │ │ │ │ │ │ $variables$returnAppropriateObj │ │ │ │ │ -[1] 149685 1286 │ │ │ │ │ +[1] 151168 1299 │ │ │ │ │ │ │ │ │ │ $variables$ssFit │ │ │ │ │ -[1] 151247 2207 │ │ │ │ │ +[1] 152752 2219 │ │ │ │ │ │ │ │ │ │ $variables$ssIntervalCandidate │ │ │ │ │ -[1] 153740 1516 │ │ │ │ │ +[1] 155265 1527 │ │ │ │ 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│ │ │ │ @@ -1,89 +1,89 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRcoefs.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRcounts.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRexperiment-class.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRexperiment2biom.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRfulltable.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRihw-fitFeatureModelResults.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRihw-fitZigResults.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRihw.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/MRtable.Rd" │ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/aggregateBySample.Rd" │ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/aggregateByTaxonomy.Rd" │ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/biom2MRexperiment.Rd" │ │ │ │ │ -[13] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calcNormFactors.Rd" │ │ │ │ │ -[14] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calcPosComponent.Rd" │ │ │ │ │ -[15] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calcShrinkParameters.Rd" │ │ │ │ │ -[16] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calcStandardError.Rd" │ │ │ │ │ -[17] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calcZeroAdjustment.Rd" │ │ │ │ │ -[18] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calcZeroComponent.Rd" │ │ │ │ │ -[19] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/calculateEffectiveSamples.Rd" │ │ │ │ │ -[20] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/correctIndices.Rd" │ │ │ │ │ -[21] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/correlationTest.Rd" │ │ │ │ │ -[22] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/cumNorm.Rd" │ │ │ │ │ -[23] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/cumNormMat.Rd" │ │ │ │ │ -[24] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/cumNormStat.Rd" │ │ │ │ │ -[25] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/cumNormStatFast.Rd" │ │ │ │ │ -[26] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/doCountMStep.Rd" │ │ │ │ │ -[27] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/doEStep.Rd" │ │ │ │ │ -[28] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/doZeroMStep.Rd" │ │ │ │ │ -[29] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/expSummary.Rd" │ │ │ │ │ -[30] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/exportMat.Rd" │ │ │ │ │ -[31] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/exportStats.Rd" │ │ │ │ │ -[32] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/extractMR.Rd" │ │ │ │ │ -[33] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/filterData.Rd" │ │ │ │ │ -[34] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitDO.Rd" │ │ │ │ │ -[35] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitFeatureModel.Rd" │ │ │ │ │ -[36] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitFeatureModelResults-class.Rd" │ │ │ │ │ -[37] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitLogNormal.Rd" │ │ │ │ │ -[38] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitMultipleTimeSeries.Rd" │ │ │ │ │ -[39] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitPA.Rd" │ │ │ │ │ -[40] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitSSTimeSeries.Rd" │ │ │ │ │ -[41] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitTimeSeries.Rd" │ │ │ │ │ -[42] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitZeroLogNormal.Rd" │ │ │ │ │ -[43] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitZig.Rd" │ │ │ │ │ -[44] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/fitZigResults-class.Rd" │ │ │ │ │ -[45] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/getCountDensity.Rd" │ │ │ │ │ -[46] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/getEpsilon.Rd" │ │ │ │ │ -[47] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/getNegativeLogLikelihoods.Rd" │ │ │ │ │ -[48] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/getPi.Rd" │ │ │ │ │ -[49] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/getZ.Rd" │ │ │ │ │ -[50] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/isItStillActive.Rd" │ │ │ │ │ -[51] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/libSize-set.Rd" │ │ │ │ │ -[52] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/libSize.Rd" │ │ │ │ │ -[53] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/loadBiom.Rd" │ │ │ │ │ -[54] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/loadMeta.Rd" │ │ │ │ │ -[55] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/loadMetaQ.Rd" │ │ │ │ │ -[56] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/loadPhenoData.Rd" │ │ │ │ │ -[57] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/lungData.Rd" │ │ │ │ │ -[58] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/makeLabels.Rd" │ │ │ │ │ -[59] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/mergeMRexperiments.Rd" │ │ │ │ │ -[60] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/mergeTable.Rd" │ │ │ │ │ -[61] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/metagenomeSeq-deprecated.Rd" │ │ │ │ │ -[62] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/metagenomeSeq-package.Rd" │ │ │ │ │ -[63] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/mouseData.Rd" │ │ │ │ │ -[64] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/newMRexperiment.Rd" │ │ │ │ │ -[65] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/normFactors-set.Rd" │ │ │ │ │ -[66] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/normFactors.Rd" │ │ │ │ │ -[67] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotBubble.Rd" │ │ │ │ │ -[68] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotClassTimeSeries.Rd" │ │ │ │ │ -[69] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotCorr.Rd" │ │ │ │ │ -[70] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotFeature.Rd" │ │ │ │ │ -[71] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotGenus.Rd" │ │ │ │ │ -[72] "/home/moeller/Salsa/r-bioc-metagenomeseq/man/plotMRheatmap.Rd" │ │ │ │ │ -[73] 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