--- /srv/rebuilderd/tmp/rebuilderdvxd4fl/inputs/r-bioc-degreport_1.48.0+dfsg-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdvxd4fl/out/r-bioc-degreport_1.48.0+dfsg-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-12 00:53:23.000000 debian-binary │ --rw-r--r-- 0 0 0 1904 2026-08-12 00:53:23.000000 control.tar.xz │ --rw-r--r-- 0 0 0 1805876 2026-08-12 00:53:23.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 1872 2026-08-12 00:53:23.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 1807400 2026-08-12 00:53:23.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:53:23.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 1263 2026-08-12 00:53:23.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 1171 2026-08-12 00:53:23.000000 ./control │ │ │ -rw-r--r-- 0 root (0) root (0) 2877 2026-08-12 00:53:23.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,14 @@ │ │ │ Package: r-bioc-degreport │ │ │ Version: 1.48.0+dfsg-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ -Installed-Size: 1912 │ │ │ +Installed-Size: 1913 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-bioc-biobase, r-bioc-biocgenerics, r-cran-broom, r-cran-circlize, r-bioc-complexheatmap, r-cran-cowplot, r-bioc-consensusclusterplus, r-cran-cluster, r-cran-dendextend, r-bioc-deseq2, r-cran-dplyr, r-bioc-edger, r-cran-ggplot2, r-cran-ggdendro, r-cran-ggrepel, r-cran-knitr, r-cran-logging, r-cran-magrittr, r-cran-psych, r-cran-rcolorbrewer, r-cran-reshape, r-cran-rlang, r-cran-scales, r-cran-stringr, r-cran-stringi, r-bioc-s4vectors, r-bioc-summarizedexperiment, r-cran-tidyr, r-cran-tibble, r-pkg-team-core-architecture │ │ │ -Suggests: r-bioc-biocstyle, r-bioc-annotationdbi, r-bioc-limma, r-cran-pheatmap, r-cran-rmarkdown, r-cran-statmod, r-cran-testthat │ │ │ +Suggests: r-bioc-limma, r-cran-statmod │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/DEGreport/ │ │ │ Description: BioConductor report of DEG analysis │ │ │ Creation of a HTML report of differential expression │ │ │ analyses of count data. It integrates some of the code │ │ │ mentioned in DESeq2 and edgeR vignettes, and report a ranked │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -15,31 +15,31 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 1352 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1964 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/Meta/package.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 286 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 3723 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 12120 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/NEWS │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/R/DEGreport │ │ │ --rw-r--r-- 0 root (0) root (0) 435953 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/R/DEGreport.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 2289 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/R/DEGreport.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 435963 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/R/DEGreport.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 2294 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/R/DEGreport.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 2098 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/README.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/data/ │ │ │ -rw-r--r-- 0 root (0) root (0) 20 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/data/datalist │ │ │ -rw-r--r-- 0 root (0) root (0) 540 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/data/geneInfo.rda │ │ │ -rw-r--r-- 0 root (0) root (0) 1298044 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/data/humanGender.rda │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 5169 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/doc/DEGreport.R │ │ │ -rw-r--r-- 0 root (0) root (0) 10349 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/doc/DEGreport.Rmd │ │ │ -rw-r--r-- 0 root (0) root (0) 1634 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/doc/index.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1122 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/help/AnIndex │ │ │ --rw-r--r-- 0 root (0) root (0) 84329 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/help/DEGreport.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 878 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/help/DEGreport.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 85259 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/help/DEGreport.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 877 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/help/DEGreport.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 477 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 389 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 406 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 6872 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/sticker/ │ │ │ -rw-r--r-- 0 root (0) root (0) 25040 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/sticker/degreport.png │ │ │ -rw-r--r-- 0 root (0) root (0) 9022 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/sticker/flag.jpg │ │ │ -rw-r--r-- 0 root (0) root (0) 2043 2026-08-12 00:53:23.000000 ./usr/lib/R/site-library/DEGreport/sticker/flag_hex.png │ │ ├── ./usr/lib/R/site-library/DEGreport/R/DEGreport.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -716,15 +716,15 @@ │ │ │ │ "imports" = " stringr = c(str_split = "str_split"), tibble = c(as_tibble = "as_tibble"), " │ │ │ │ "imports" = " tibble = c(column_to_rownames = "column_to_rownames"), tibble = c(remove_rownames = "remove_rownames"), " │ │ │ │ "imports" = " tibble = c(rownames_to_column = "rownames_to_column"), tidyr = c(gather = "gather"), " │ │ │ │ "imports" = " tidyr = c(spread = "spread"), tidyr = c(unite = "unite"), " │ │ │ │ "imports" = " BiocGenerics = c(".__T__plotMA:BiocGenerics" = ".__T__plotMA:BiocGenerics", " │ │ │ │ "imports" = " plotMA = "plotMA"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-degreport/debian/r-bioc-degreport/usr/lib/R/site-library/DEGreport"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/debian/r-bioc-degreport/usr/lib/R/site-library/DEGreport"" │ │ │ │ "spec" = "c(name = "DEGreport", version = "1.48.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/DEGreport/R/DEGreport.rdx │ │ │ ├── DEGreport.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,520 +1,520 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$.__C__DEGSet │ │ │ │ │ [1] 0 2032 │ │ │ │ │ │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 12139 52 │ │ │ │ │ +[1] 12149 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 12322 52 │ │ │ │ │ +[1] 12332 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__as.DEGSet:DEGreport` │ │ │ │ │ -[1] 17602 52 │ │ │ │ │ +[1] 17612 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__deg:DEGreport` │ │ │ │ │ -[1] 23284 52 │ │ │ │ │ +[1] 23294 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__degCorrect:DEGreport` │ │ │ │ │ -[1] 26270 53 │ │ │ │ │ +[1] 26280 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__degDefault:DEGreport` │ │ │ │ │ -[1] 27919 53 │ │ │ │ │ +[1] 27929 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__show:methods` │ │ │ │ │ -[1] 247005 53 │ │ │ │ │ +[1] 247015 53 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__significants:DEGreport` │ │ │ │ │ -[1] 256795 53 │ │ │ │ │ +[1] 256805 53 │ │ │ │ │ │ │ │ │ │ $variables$.__global__ │ │ │ │ │ -[1] 256848 54 │ │ │ │ │ +[1] 256858 54 │ │ │ │ │ │ │ │ │ │ $variables$.benckmark_cutoff │ │ │ │ │ -[1] 256902 2011 │ │ │ │ │ +[1] 256912 2011 │ │ │ │ │ │ │ │ │ │ $variables$.calccompletecorandplot │ │ │ │ │ -[1] 258913 2957 │ │ │ │ │ +[1] 258923 2957 │ │ │ │ │ │ │ │ │ │ $variables$.convertIDs │ │ │ │ │ -[1] 261870 1320 │ │ │ │ │ +[1] 261880 1320 │ │ │ │ │ │ │ │ │ │ $variables$.correct_fdr │ │ │ │ │ -[1] 263190 1421 │ │ │ │ │ +[1] 263200 1421 │ │ │ │ │ │ │ │ │ │ $variables$.createComb │ │ │ │ │ -[1] 264611 753 │ │ │ │ │ +[1] 264621 753 │ │ │ │ │ │ │ │ │ │ $variables$.effect_size │ │ │ │ │ -[1] 265364 1430 │ │ │ │ │ +[1] 265374 1430 │ │ │ │ │ │ │ │ │ │ $variables$.filter │ │ │ │ │ -[1] 266794 517 │ │ │ │ │ +[1] 266804 517 │ │ │ │ │ │ │ │ │ │ $variables$.filterTable │ │ │ │ │ -[1] 267311 901 │ │ │ │ │ +[1] 267321 901 │ │ │ │ │ │ │ │ │ │ $variables$.find_pattern │ │ │ │ │ -[1] 268212 1292 │ │ │ │ │ +[1] 268222 1292 │ │ │ │ │ │ │ │ │ │ $variables$.generate_scatter_plot │ │ │ │ │ -[1] 269504 1553 │ │ │ │ │ +[1] 269514 1553 │ │ │ │ │ │ │ │ │ │ $variables$.get_contrast_name │ │ │ │ │ -[1] 271057 995 │ │ │ │ │ +[1] 271067 995 │ │ │ │ │ │ │ │ │ │ $variables$.get_counts │ │ │ │ │ -[1] 272052 1066 │ │ │ │ │ +[1] 272062 1066 │ │ │ │ │ │ │ │ │ │ $variables$.get_features │ │ │ │ │ -[1] 273118 745 │ │ │ │ │ +[1] 273128 745 │ │ │ │ │ │ │ │ │ │ $variables$.get_meta │ │ │ │ │ -[1] 273863 586 │ │ │ │ │ +[1] 273873 586 │ │ │ │ │ │ │ │ │ │ $variables$.getfactorcontassociationstatistics │ │ │ │ │ -[1] 274449 1093 │ │ │ │ │ +[1] 274459 1093 │ │ │ │ │ │ │ │ │ │ $variables$.group_metadata │ │ │ │ │ -[1] 275542 1079 │ │ │ │ │ +[1] 275552 1079 │ │ │ │ │ │ │ │ │ │ $variables$.guessComb │ │ │ │ │ -[1] 276621 2185 │ │ │ │ │ +[1] 276631 2185 │ │ │ │ │ │ │ │ │ │ $variables$.guessResults │ │ │ │ │ -[1] 278806 1073 │ │ │ │ │ +[1] 278816 1073 │ │ │ │ │ │ │ │ │ │ $variables$.guessShrunken │ │ │ │ │ -[1] 279879 1327 │ │ │ │ │ +[1] 279889 1327 │ │ │ │ │ │ │ │ │ │ $variables$.integrate │ │ │ │ │ -[1] 281206 2503 │ │ │ │ │ +[1] 281216 2503 │ │ │ │ │ │ │ │ │ │ $variables$.logger │ │ │ │ │ -[1] 283709 483 │ │ │ │ │ +[1] 283719 483 │ │ │ │ │ │ │ │ │ │ $variables$.make_clusters │ │ │ │ │ -[1] 284192 559 │ │ │ │ │ +[1] 284202 559 │ │ │ │ │ │ │ │ │ │ $variables$.make_concensus_cluster │ │ │ │ │ -[1] 284751 415 │ │ │ │ │ +[1] 284761 415 │ │ │ │ │ │ │ │ │ │ $variables$.median_per_cluster │ │ │ │ │ -[1] 285166 1236 │ │ │ │ │ +[1] 285176 1236 │ │ │ │ │ │ │ │ │ │ $variables$.merge_results │ │ │ │ │ -[1] 286402 1257 │ │ │ │ │ +[1] 286412 1257 │ │ │ │ │ │ │ │ │ │ $variables$.model │ │ │ │ │ -[1] 287659 677 │ │ │ │ │ +[1] 287669 677 │ │ │ │ │ │ │ │ │ │ $variables$.normalizeNames │ │ │ │ │ -[1] 288336 678 │ │ │ │ │ +[1] 288346 678 │ │ │ │ │ │ │ │ │ │ $variables$.numeric_effect_size │ │ │ │ │ -[1] 289014 963 │ │ │ │ │ +[1] 289024 963 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 289977 54 │ │ │ │ │ +[1] 289987 54 │ │ │ │ │ │ │ │ │ │ $variables$.pca_loadings │ │ │ │ │ -[1] 290031 691 │ │ │ │ │ +[1] 290041 691 │ │ │ │ │ │ │ │ │ │ $variables$.pct_var │ │ │ │ │ -[1] 290722 939 │ │ │ │ │ +[1] 290732 939 │ │ │ │ │ │ │ │ │ │ $variables$.plot_base │ │ │ │ │ -[1] 291661 1238 │ │ │ │ │ +[1] 291671 1238 │ │ │ │ │ │ │ │ │ │ $variables$.plot_benchmarking │ │ │ │ │ -[1] 292899 2341 │ │ │ │ │ +[1] 292909 2341 │ │ │ │ │ │ │ │ │ │ $variables$.plot_benchmarking_curve │ │ │ │ │ -[1] 295240 1613 │ │ │ │ │ +[1] 295250 1613 │ │ │ │ │ │ │ │ │ │ $variables$.plot_cluster │ │ │ │ │ -[1] 296853 1738 │ │ │ │ │ +[1] 296863 1738 │ │ │ │ │ │ │ │ │ │ $variables$.plot_correlation │ │ │ │ │ -[1] 298591 920 │ │ │ │ │ +[1] 298601 920 │ │ │ │ │ │ │ │ │ │ $variables$.plot_raw │ │ │ │ │ -[1] 299511 1530 │ │ │ │ │ +[1] 299521 1530 │ │ │ │ │ │ │ │ │ │ $variables$.plot_shrunken │ │ │ │ │ -[1] 301041 1733 │ │ │ │ │ +[1] 301051 1733 │ │ │ │ │ │ │ │ │ │ $variables$.process │ │ │ │ │ -[1] 302774 1141 │ │ │ │ │ +[1] 302784 1141 │ │ │ │ │ │ │ │ │ │ $variables$.reduce │ │ │ │ │ -[1] 303915 1389 │ │ │ │ │ +[1] 303925 1389 │ │ │ │ │ │ │ │ │ │ $variables$.reduce_covariates │ │ │ │ │ -[1] 305304 2332 │ │ │ │ │ +[1] 305314 2332 │ │ │ │ │ │ │ │ │ │ $variables$.remove_low_difference │ │ │ │ │ -[1] 307636 1381 │ │ │ │ │ +[1] 307646 1381 │ │ │ │ │ │ │ │ │ │ $variables$.requireCachedGenerics │ │ │ │ │ -[1] 309017 75 │ │ │ │ │ +[1] 309027 75 │ │ │ │ │ │ │ │ │ │ $variables$.run_cluster_profiler │ │ │ │ │ -[1] 309092 1531 │ │ │ │ │ +[1] 309102 1531 │ │ │ │ │ │ │ │ │ │ $variables$.runpca │ │ │ │ │ -[1] 310623 917 │ │ │ │ │ +[1] 310633 917 │ │ │ │ │ │ │ │ │ │ $variables$.save_file │ │ │ │ │ -[1] 311540 822 │ │ │ │ │ +[1] 311550 822 │ │ │ │ │ │ │ │ │ │ $variables$.scale │ │ │ │ │ -[1] 312362 225 │ │ │ │ │ +[1] 312372 225 │ │ │ │ │ │ │ │ │ │ $variables$.select_concensus_genes │ │ │ │ │ -[1] 312587 1292 │ │ │ │ │ +[1] 312597 1292 │ │ │ │ │ │ │ │ │ │ $variables$.select_genes │ │ │ │ │ -[1] 313879 1078 │ │ │ │ │ +[1] 313889 1078 │ │ │ │ │ │ │ │ │ │ $variables$.select_pattern │ │ │ │ │ -[1] 314957 838 │ │ │ │ │ +[1] 314967 838 │ │ │ │ │ │ │ │ │ │ $variables$.summarise_res │ │ │ │ │ -[1] 315795 1733 │ │ │ │ │ +[1] 315805 1733 │ │ │ │ │ │ │ │ │ │ $variables$.summarize_scale │ │ │ │ │ -[1] 317528 1259 │ │ │ │ │ +[1] 317538 1259 │ │ │ │ │ │ │ │ │ │ $variables$.summary │ │ │ │ │ -[1] 318787 1383 │ │ │ │ │ +[1] 318797 1383 │ │ │ │ │ │ │ │ │ │ $variables$.supported │ │ │ │ │ -[1] 320170 358 │ │ │ │ │ +[1] 320180 358 │ │ │ │ │ │ │ │ │ │ $variables$.table_w_fc │ │ │ │ │ -[1] 320528 1633 │ │ │ │ │ +[1] 320538 1633 │ │ │ │ │ │ │ │ │ │ $variables$.validate │ │ │ │ │ -[1] 322161 498 │ │ │ │ │ +[1] 322171 498 │ │ │ │ │ │ │ │ │ │ $variables$DEGSet │ │ │ │ │ -[1] 322659 483 │ │ │ │ │ +[1] 322669 483 │ │ │ │ │ │ │ │ │ │ $variables$GeomCor │ │ │ │ │ -[1] 340710 53 │ │ │ │ │ +[1] 340720 53 │ │ │ │ │ │ │ │ │ │ $variables$StatCor │ │ │ │ │ -[1] 350238 53 │ │ │ │ │ +[1] 350248 53 │ │ │ │ │ │ │ │ │ │ $variables$as.DEGSet │ │ │ │ │ -[1] 350291 417 │ │ │ │ │ +[1] 350301 417 │ │ │ │ │ │ │ │ │ │ $variables$createReport │ │ │ │ │ -[1] 350708 303 │ │ │ │ │ +[1] 350718 303 │ │ │ │ │ │ │ │ │ │ $variables$deg │ │ │ │ │ -[1] 351011 465 │ │ │ │ │ +[1] 351021 465 │ │ │ │ │ │ │ │ │ │ $variables$degBI │ │ │ │ │ -[1] 351476 217 │ │ │ │ │ +[1] 351486 217 │ │ │ │ │ │ │ │ │ │ $variables$degBIcmd │ │ │ │ │ -[1] 351693 217 │ │ │ │ │ +[1] 351703 217 │ │ │ │ │ │ │ │ │ │ $variables$degCheckFactors │ │ │ │ │ -[1] 351910 1798 │ │ │ │ │ +[1] 351920 1798 │ │ │ │ │ │ │ │ │ │ $variables$degClean │ │ │ │ │ -[1] 353708 1723 │ │ │ │ │ +[1] 353718 1723 │ │ │ │ │ │ │ │ │ │ $variables$degColors │ │ │ │ │ -[1] 355431 1626 │ │ │ │ │ +[1] 355441 1626 │ │ │ │ │ │ │ │ │ │ $variables$degComb │ │ │ │ │ -[1] 357057 217 │ │ │ │ │ +[1] 357067 217 │ │ │ │ │ │ │ │ │ │ $variables$degComps │ │ │ │ │ -[1] 357274 2269 │ │ │ │ │ +[1] 357284 2269 │ │ │ │ │ │ │ │ │ │ $variables$degCorCov │ │ │ │ │ -[1] 359543 2057 │ │ │ │ │ +[1] 359553 2057 │ │ │ │ │ │ │ │ │ │ $variables$degCorrect │ │ │ │ │ -[1] 361600 430 │ │ │ │ │ +[1] 361610 430 │ │ │ │ │ │ │ │ │ │ $variables$degCovariates │ │ │ │ │ -[1] 362030 9723 │ │ │ │ │ +[1] 362040 9723 │ │ │ │ │ │ │ │ │ │ $variables$degDefault │ │ │ │ │ -[1] 371753 401 │ │ │ │ │ +[1] 371763 401 │ │ │ │ │ │ │ │ │ │ $variables$degFC │ │ │ │ │ -[1] 372154 217 │ │ │ │ │ +[1] 372164 217 │ │ │ │ │ │ │ │ │ │ $variables$degFilter │ │ │ │ │ -[1] 372371 999 │ │ │ │ │ +[1] 372381 999 │ │ │ │ │ │ │ │ │ │ $variables$degMA │ │ │ │ │ -[1] 373370 2539 │ │ │ │ │ +[1] 373380 2539 │ │ │ │ │ │ │ │ │ │ $variables$degMB │ │ │ │ │ -[1] 375909 1879 │ │ │ │ │ +[1] 375919 1879 │ │ │ │ │ │ │ │ │ │ $variables$degMDS │ │ │ │ │ -[1] 377788 2331 │ │ │ │ │ +[1] 377798 2331 │ │ │ │ │ │ │ │ │ │ $variables$degMV │ │ │ │ │ -[1] 380119 2292 │ │ │ │ │ +[1] 380129 2292 │ │ │ │ │ │ │ │ │ │ $variables$degMean │ │ │ │ │ -[1] 382411 1412 │ │ │ │ │ +[1] 382421 1412 │ │ │ │ │ │ │ │ │ │ $variables$degMerge │ │ │ │ │ -[1] 383823 4154 │ │ │ │ │ +[1] 383833 4154 │ │ │ │ │ │ │ │ │ │ $variables$degNcomb │ │ │ │ │ -[1] 387977 217 │ │ │ │ │ +[1] 387987 217 │ │ │ │ │ │ │ │ │ │ $variables$degObj │ │ │ │ │ -[1] 388194 530 │ │ │ │ │ +[1] 388204 530 │ │ │ │ │ │ │ │ │ │ $variables$degPCA │ │ │ │ │ -[1] 388724 2276 │ │ │ │ │ +[1] 388734 2276 │ │ │ │ │ │ │ │ │ │ $variables$degPR │ │ │ │ │ -[1] 391000 217 │ │ │ │ │ +[1] 391010 217 │ │ │ │ │ │ │ │ │ │ $variables$degPatterns │ │ │ │ │ -[1] 391217 9466 │ │ │ │ │ +[1] 391227 9466 │ │ │ │ │ │ │ │ │ │ $variables$degPlot │ │ │ │ │ -[1] 400683 6101 │ │ │ │ │ +[1] 400693 6101 │ │ │ │ │ │ │ │ │ │ $variables$degPlotCluster │ │ │ │ │ -[1] 406784 4077 │ │ │ │ │ +[1] 406794 4077 │ │ │ │ │ │ │ │ │ │ $variables$degPlotWide │ │ │ │ │ -[1] 410861 2875 │ │ │ │ │ +[1] 410871 2875 │ │ │ │ │ │ │ │ │ │ $variables$degQC │ │ │ │ │ -[1] 413736 2694 │ │ │ │ │ +[1] 413746 2694 │ │ │ │ │ │ │ │ │ │ $variables$degRank │ │ │ │ │ -[1] 416430 217 │ │ │ │ │ +[1] 416440 217 │ │ │ │ │ │ │ │ │ │ $variables$degResults │ │ │ │ │ -[1] 416647 5399 │ │ │ │ │ +[1] 416657 5399 │ │ │ │ │ │ │ │ │ │ $variables$degSignature │ │ │ │ │ -[1] 422046 2149 │ │ │ │ │ +[1] 422056 2149 │ │ │ │ │ │ │ │ │ │ $variables$degSummary │ │ │ │ │ -[1] 424195 1689 │ │ │ │ │ +[1] 424205 1689 │ │ │ │ │ │ │ │ │ │ $variables$degVB │ │ │ │ │ -[1] 425884 1862 │ │ │ │ │ +[1] 425894 1862 │ │ │ │ │ │ │ │ │ │ $variables$degVar │ │ │ │ │ -[1] 427746 1414 │ │ │ │ │ +[1] 427756 1414 │ │ │ │ │ │ │ │ │ │ $variables$degVolcano │ │ │ │ │ -[1] 429160 4604 │ │ │ │ │ +[1] 429170 4604 │ │ │ │ │ │ │ │ │ │ $variables$figurebyexp │ │ │ │ │ -[1] 433764 285 │ │ │ │ │ +[1] 433774 285 │ │ │ │ │ │ │ │ │ │ $variables$figurebyvar │ │ │ │ │ -[1] 434049 285 │ │ │ │ │ +[1] 434059 285 │ │ │ │ │ │ │ │ │ │ $variables$figurepvaluebyvarexp │ │ │ │ │ -[1] 434334 275 │ │ │ │ │ +[1] 434344 275 │ │ │ │ │ │ │ │ │ │ $variables$fmt │ │ │ │ │ -[1] 434609 330 │ │ │ │ │ +[1] 434619 330 │ │ │ │ │ │ │ │ │ │ $variables$geom_cor │ │ │ │ │ -[1] 434939 499 │ │ │ │ │ +[1] 434949 499 │ │ │ │ │ │ │ │ │ │ $variables$significants │ │ │ │ │ -[1] 435438 515 │ │ │ │ │ +[1] 435448 515 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 2324 9815 │ │ │ │ │ +[1] 2324 9825 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 21224 275 │ │ │ │ │ +[1] 21234 275 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 17654 1785 │ │ │ │ │ +[1] 17664 1785 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 19439 1785 │ │ │ │ │ +[1] 19449 1785 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 25381 889 │ │ │ │ │ +[1] 25391 889 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 25114 267 │ │ │ │ │ +[1] 25124 267 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 23336 889 │ │ │ │ │ +[1] 23346 889 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 24225 889 │ │ │ │ │ +[1] 24235 889 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 27474 445 │ │ │ │ │ +[1] 27484 445 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 27213 261 │ │ │ │ │ +[1] 27223 261 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 26323 445 │ │ │ │ │ +[1] 26333 445 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 2032 131 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 26768 445 │ │ │ │ │ +[1] 26778 445 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 246313 692 │ │ │ │ │ +[1] 246323 692 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 245854 459 │ │ │ │ │ +[1] 245864 459 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 151812 47021 │ │ │ │ │ +[1] 151822 47021 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 27972 170 │ │ │ │ │ +[1] 27982 170 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 28142 1516 │ │ │ │ │ +[1] 28152 1516 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ -[1] 149339 2473 │ │ │ │ │ +[1] 149349 2473 │ │ │ │ │ │ │ │ │ │ $references$`env::27` │ │ │ │ │ -[1] 134894 143 │ │ │ │ │ +[1] 134904 143 │ │ │ │ │ │ │ │ │ │ $references$`env::28` │ │ │ │ │ -[1] 129765 5129 │ │ │ │ │ +[1] 129775 5129 │ │ │ │ │ │ │ │ │ │ $references$`env::29` │ │ │ │ │ -[1] 129044 721 │ │ │ │ │ +[1] 129054 721 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 2163 161 │ │ │ │ │ │ │ │ │ │ $references$`env::30` │ │ │ │ │ -[1] 38395 143 │ │ │ │ │ +[1] 38405 143 │ │ │ │ │ │ │ │ │ │ $references$`env::31` │ │ │ │ │ -[1] 29658 8737 │ │ │ │ │ +[1] 29668 8737 │ │ │ │ │ │ │ │ │ │ $references$`env::32` │ │ │ │ │ -[1] 124286 4758 │ │ │ │ │ +[1] 124296 4758 │ │ │ │ │ │ │ │ │ │ $references$`env::33` │ │ │ │ │ -[1] 54391 43807 │ │ │ │ │ +[1] 54401 43807 │ │ │ │ │ │ │ │ │ │ $references$`env::34` │ │ │ │ │ -[1] 46633 336 │ │ │ │ │ +[1] 46643 336 │ │ │ │ │ │ │ │ │ │ $references$`env::35` │ │ │ │ │ -[1] 39629 7004 │ │ │ │ │ +[1] 39639 7004 │ │ │ │ │ │ │ │ │ │ $references$`env::36` │ │ │ │ │ -[1] 38538 1091 │ │ │ │ │ +[1] 38548 1091 │ │ │ │ │ │ │ │ │ │ $references$`env::37` │ │ │ │ │ -[1] 46969 2269 │ │ │ │ │ +[1] 46979 2269 │ │ │ │ │ │ │ │ │ │ $references$`env::38` │ │ │ │ │ -[1] 49238 4845 │ │ │ │ │ +[1] 49248 4845 │ │ │ │ │ │ │ │ │ │ $references$`env::39` │ │ │ │ │ -[1] 54083 308 │ │ │ │ │ +[1] 54093 308 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 12191 131 │ │ │ │ │ +[1] 12201 131 │ │ │ │ │ │ │ │ │ │ $references$`env::40` │ │ │ │ │ -[1] 98198 26088 │ │ │ │ │ +[1] 98208 26088 │ │ │ │ │ │ │ │ │ │ $references$`env::41` │ │ │ │ │ -[1] 140830 2511 │ │ │ │ │ +[1] 140840 2511 │ │ │ │ │ │ │ │ │ │ $references$`env::42` │ │ │ │ │ -[1] 140671 159 │ │ │ │ │ +[1] 140681 159 │ │ │ │ │ │ │ │ │ │ $references$`env::43` │ │ │ │ │ -[1] 135037 5634 │ │ │ │ │ +[1] 135047 5634 │ │ │ │ │ │ │ │ │ │ $references$`env::44` │ │ │ │ │ -[1] 149196 143 │ │ │ │ │ +[1] 149206 143 │ │ │ │ │ │ │ │ │ │ $references$`env::45` │ │ │ │ │ -[1] 144065 5131 │ │ │ │ │ +[1] 144075 5131 │ │ │ │ │ │ │ │ │ │ $references$`env::46` │ │ │ │ │ -[1] 143341 724 │ │ │ │ │ +[1] 143351 724 │ │ │ │ │ │ │ │ │ │ $references$`env::47` │ │ │ │ │ -[1] 198833 47021 │ │ │ │ │ +[1] 198843 47021 │ │ │ │ │ │ │ │ │ │ $references$`env::48` │ │ │ │ │ -[1] 253645 3150 │ │ │ │ │ +[1] 253655 3150 │ │ │ │ │ │ │ │ │ │ $references$`env::49` │ │ │ │ │ -[1] 253358 287 │ │ │ │ │ +[1] 253368 287 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 15946 1656 │ │ │ │ │ +[1] 15956 1656 │ │ │ │ │ │ │ │ │ │ $references$`env::50` │ │ │ │ │ -[1] 247058 3150 │ │ │ │ │ +[1] 247068 3150 │ │ │ │ │ │ │ │ │ │ $references$`env::51` │ │ │ │ │ -[1] 250208 3150 │ │ │ │ │ +[1] 250218 3150 │ │ │ │ │ │ │ │ │ │ $references$`env::52` │ │ │ │ │ -[1] 336677 4033 │ │ │ │ │ +[1] 336687 4033 │ │ │ │ │ │ │ │ │ │ $references$`env::53` │ │ │ │ │ -[1] 323142 550 │ │ │ │ │ +[1] 323152 550 │ │ │ │ │ │ │ │ │ │ $references$`env::54` │ │ │ │ │ -[1] 332325 4352 │ │ │ │ │ +[1] 332335 4352 │ │ │ │ │ │ │ │ │ │ $references$`env::55` │ │ │ │ │ -[1] 323692 8633 │ │ │ │ │ +[1] 323702 8633 │ │ │ │ │ │ │ │ │ │ $references$`env::56` │ │ │ │ │ -[1] 348667 1571 │ │ │ │ │ +[1] 348677 1571 │ │ │ │ │ │ │ │ │ │ $references$`env::57` │ │ │ │ │ -[1] 346772 1895 │ │ │ │ │ +[1] 346782 1895 │ │ │ │ │ │ │ │ │ │ $references$`env::58` │ │ │ │ │ -[1] 340763 6009 │ │ │ │ │ +[1] 340773 6009 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 15686 260 │ │ │ │ │ +[1] 15696 260 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 12374 1656 │ │ │ │ │ +[1] 12384 1656 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 14030 1656 │ │ │ │ │ +[1] 14040 1656 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 21499 1785 │ │ │ │ │ +[1] 21509 1785 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/DEGreport/help/DEGreport.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -74,15 +74,15 @@ │ │ │ │ structure("dds <- DESeq(dds)\n", Rd_tag = "RCODE"), structure("res <- degComps(dds, combs = c(\"condition\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("deg(res)\n", Rd_tag = "RCODE"), structure("deg(res, tidy = \"tibble\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# From edgeR\n", Rd_tag = "RCODE"), structure("dge <- DGEList(counts=counts(dds), group=colData(dds)[[\"treatment\"]])\n", Rd_tag = "RCODE"), │ │ │ │ structure("dge <- estimateCommonDisp(dge)\n", Rd_tag = "RCODE"), │ │ │ │ structure("res <- as.DEGSet(topTags(exactTest(dge)))\n", Rd_tag = "RCODE"), │ │ │ │ structure("# From limma\n", Rd_tag = "RCODE"), structure("v <- voom(counts(dds), model.matrix(~treatment, colData(dds)), plot=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("fit <- lmFit(v)\n", Rd_tag = "RCODE"), structure("fit <- eBayes(fit, robust=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("res <- as.DEGSet(topTable(fit, n = \"Inf\"), \"A_vs_B\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/DEGSet.Rd", class = "Rd", meta = list( │ │ │ │ + structure("res <- as.DEGSet(topTable(fit, n = \"Inf\"), \"A_vs_B\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/DEGSet.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ DEGreport-deprecated (list) = structure(list(structure(list(structure("Deprecated functions in package DEGreport", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("DEGreport-package", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("DEGreport", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("DEGreport-package", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("These functions are provided for compatibility with older versions\n", Rd_tag = "TEXT"), │ │ │ │ @@ -124,15 +124,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(), Rd_tag = "\\item"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("http://lpantano.github.io/DEGreport/", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(), Rd_tag = "\\item"), structure(" Report bugs at ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("https://github.com/lpantano/DEGreport/issues", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ - structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/DEGreport-deprecated.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/DEGreport-deprecated.Rd", class = "Rd", meta = list( │ │ │ │ docType = "package", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ createReport (list) = structure(list(structure(list(structure("Create report of RNAseq DEG anlaysis", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("createReport", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("createReport", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function get the count matrix, pvalues, and FC of a\n", Rd_tag = "TEXT"), │ │ │ │ structure("DEG analysis and create a report to help to detect possible problems\n", Rd_tag = "TEXT"), │ │ │ │ @@ -156,15 +156,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("pop", Rd_tag = "TEXT")), │ │ │ │ list(structure("random genes for background", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("name", Rd_tag = "TEXT")), │ │ │ │ list(structure("name of the html file", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("A HTML file with all figures and tables\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/createReport.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("A HTML file with all figures and tables\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/createReport.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ deg (list) = structure(list(structure(list(structure("Method to get all table stored for an specific comparison", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("deg", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("deg", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("deg,DEGSet-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Method to get all table stored for an specific comparison\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -191,15 +191,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Lorena Pantano\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(), Rd_tag = "\\item"), │ │ │ │ structure(" Testing if ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("top", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" is whole number or not comes from:\n", Rd_tag = "TEXT"), │ │ │ │ structure("https://stackoverflow.com/a/3477158\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/deg.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/deg.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degCheckFactors (list) = structure(list(structure(list(structure("Distribution of gene ratios used to calculate Size Factors.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degCheckFactors", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degCheckFactors", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function check the median ratio normalization used by\n", Rd_tag = "TEXT"), │ │ │ │ structure("DESeq2 and similarly by edgeR to visualy check whether\n", Rd_tag = "TEXT"), │ │ │ │ @@ -223,15 +223,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(), Rd_tag = "\\item"), │ │ │ │ structure(" Code to calculate size factors comes from\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("DESeq2::estimateSizeFactorsForMatrix()", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("DESeq2:estimateSizeFactorsForMatrix", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(SummarizedExperiment)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("degCheckFactors(assays(humanGender)[[1]][, 1:10])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degCheckFactors.Rd", class = "Rd", meta = list( │ │ │ │ + structure("degCheckFactors(assays(humanGender)[[1]][, 1:10])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degCheckFactors.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degColors (list) = structure(list(structure(list(structure("Make nice colors for metadata", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degColors", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degColors", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The function will take a metadata table and use Set2 palette when\n", Rd_tag = "TEXT"), │ │ │ │ structure("number of levels is > 3 or a set or orange/blue colors other wise.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -273,15 +273,15 @@ │ │ │ │ structure("Heatmap(log2(counts(dse)+0.5), top_annotation = th)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("custom <- degColors(colData(dse), TRUE,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" con_values = c(\"white\", \"red\"),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" cat_values = c(\"white\", \"black\"),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" palette = \"Set1\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("th <- HeatmapAnnotation(df = colData(dse),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" col = custom)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("Heatmap(log2(counts(dse)+0.5), top_annotation = th)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degColors.Rd", class = "Rd", meta = list( │ │ │ │ + structure("Heatmap(log2(counts(dse)+0.5), top_annotation = th)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degColors.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degComps (list) = structure(list(structure(list(structure("Automatize the use of ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("results()", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" for multiple comparisons", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degComps", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degComps", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -363,15 +363,15 @@ │ │ │ │ structure("dds <- makeExampleDESeqDataSet(betaSD=1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("colData(dds)[[\"treatment\"]] <- sample(colData(dds)[[\"condition\"]], 12)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" design(dds) <- ~ condition + treatment\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeq(dds)\n", Rd_tag = "RCODE"), structure("res <- degComps(dds, combs = c(\"condition\", 2),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" contrast = list(\"treatment_B_vs_A\", c(\"condition\", \"A\", \"B\")))\n", Rd_tag = "RCODE"), │ │ │ │ structure("# library(fdrtools)\n", Rd_tag = "RCODE"), │ │ │ │ structure("#res <- degComps(dds,contrast = list(\"treatment_B_vs_A\"),\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# fdr=\"lfdr-stat\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degComps.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# fdr=\"lfdr-stat\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degComps.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degCorCov (list) = structure(list(structure(list(structure("Calculate the correlation relationshipt among all covariates\n", Rd_tag = "TEXT"), │ │ │ │ structure("in the metadata table", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degCorCov", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degCorCov", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function will calculate the correlation among\n", Rd_tag = "TEXT"), │ │ │ │ @@ -400,15 +400,15 @@ │ │ │ │ structure("c) fdrMat, data.frame with FDR matrix\n", Rd_tag = "TEXT"), │ │ │ │ structure("b) plot, Heatmap plot of correlation matrix\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(": Lorena Pantano, Kenneth Daily and Thanneer Malai Perumal\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(DESeq2)\n", Rd_tag = "RCODE"), structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(humanGender)[idx,], design=~group)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("cor <- degCorCov(colData(dse))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degCorCov.Rd", class = "Rd", meta = list( │ │ │ │ + structure("cor <- degCorCov(colData(dse))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degCorCov.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degCovariates (list) = structure(list(structure(list(structure("Find correlation between pcs and covariates", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degCovariates", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degCovariates", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function will calculate the pcs using prcomp function,\n", Rd_tag = "TEXT"), │ │ │ │ structure("and correlate categorical and numerical variables from\n", Rd_tag = "TEXT"), │ │ │ │ @@ -534,15 +534,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(DESeq2)\n", Rd_tag = "RCODE"), structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(humanGender)[idx,], design=~group)\n", Rd_tag = "RCODE"), │ │ │ │ structure("res <- degCovariates(log2(counts(dse)+0.5), colData(dse))\n", Rd_tag = "RCODE"), │ │ │ │ structure("res <- degCovariates(log2(counts(dse)+0.5),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(dse), legacy = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("res$plot\n", Rd_tag = "RCODE"), structure("res$scatterPlot[[1]]\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degCovariates.Rd", class = "Rd", meta = list( │ │ │ │ + structure("res$plot\n", Rd_tag = "RCODE"), structure("res$scatterPlot[[1]]\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degCovariates.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degDefault (list) = structure(list(structure(list(structure("Method to get the default table to use.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degDefault", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degDefault", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("degCorrect", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("degDefault,DEGSet-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -569,15 +569,15 @@ │ │ │ │ structure(", vector of new padj", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Lorena Pantano\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("library(DESeq2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(dplyr)\n", Rd_tag = "RCODE"), structure("dds <- makeExampleDESeqDataSet(betaSD=1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("colData(dds)[[\"treatment\"]] <- sample(colData(dds)[[\"condition\"]], 12)\n", Rd_tag = "RCODE"), │ │ │ │ structure("design(dds) <- ~ condition + treatment\n", Rd_tag = "RCODE"), │ │ │ │ - structure("dds <- DESeq(dds)\n", Rd_tag = "RCODE"), structure("res <- degComps(dds, contrast = list(\"treatment_B_vs_A\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degDefault.Rd", class = "Rd", meta = list( │ │ │ │ + structure("dds <- DESeq(dds)\n", Rd_tag = "RCODE"), structure("res <- degComps(dds, contrast = list(\"treatment_B_vs_A\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degDefault.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degFilter (list) = structure(list(structure(list(structure("Filter genes by group", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degFilter", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degFilter", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function will keep only rows that have a minimum counts of\n", Rd_tag = "TEXT"), │ │ │ │ structure("1 at least in a ", Rd_tag = "TEXT"), structure(list( │ │ │ │ @@ -611,15 +611,15 @@ │ │ │ │ structure(list(structure("matrix", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" after filtering genes (features)\n", Rd_tag = "TEXT"), │ │ │ │ structure("with not enough expression in any group.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(SummarizedExperiment)\n", Rd_tag = "RCODE"), │ │ │ │ structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("c <- degFilter(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" colData(humanGender)[idx,], \"group\", min=1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degFilter.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" colData(humanGender)[idx,], \"group\", min=1)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degFilter.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degMA (list) = structure(list(structure(list(structure("MA-plot from base means and log fold changes", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degMA", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degMA", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("MA-plot addaptation to show the shrinking effect.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("degMA(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -662,15 +662,15 @@ │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Victor Barrera\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("Rory Kirchner\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("Lorena Pantano\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("library(DESeq2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- makeExampleDESeqDataSet(betaSD=1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeq(dds)\n", Rd_tag = "RCODE"), structure("res <- degComps(dds, contrast = list(\"condition_B_vs_A\"))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("degMA(res)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degMA.Rd", class = "Rd", meta = list( │ │ │ │ + structure("degMA(res)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degMA.Rd", class = "Rd", meta = list( │ │ │ │ docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degMB (list) = structure(list(structure(list(structure("Distribution of expression of DE genes compared to the background", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degMB", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degMB", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Distribution of expression of DE genes compared to the background\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("degMB(tags, group, counts, pop = 400)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -691,15 +691,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("ggplot2 object\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(DESeq2)\n", Rd_tag = "RCODE"), structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(humanGender)[idx,], design=~group)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeq(dds)\n", Rd_tag = "RCODE"), structure("res <- results(dds)\n", Rd_tag = "RCODE"), │ │ │ │ structure("degMB(row.names(res)[1:20], colData(dds)[[\"group\"]],\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" counts(dds, normalized = TRUE))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degMB.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" counts(dds, normalized = TRUE))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degMB.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degMDS (list) = structure(list(structure(list(structure("Plot MDS from normalized count data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degMDS", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degMDS", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Uses cmdscale to get multidimensional scaling of data matrix,\n", Rd_tag = "TEXT"), │ │ │ │ structure("and plot the samples with ggplot2.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -724,15 +724,15 @@ │ │ │ │ list(structure("number of component to plot in y-axis", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("ggplot2 object\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(DESeq2)\n", Rd_tag = "RCODE"), structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(humanGender)[idx,], design=~group)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("degMDS(counts(dse), condition = colData(dse)[[\"group\"]])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degMDS.Rd", class = "Rd", meta = list( │ │ │ │ + structure("degMDS(counts(dse), condition = colData(dse)[[\"group\"]])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degMDS.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degMV (list) = structure(list(structure(list(structure("Correlation of the standard desviation and the mean of the abundance of a\n", Rd_tag = "TEXT"), │ │ │ │ structure("set of genes.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degMV", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degMV", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Correlation of the standard desviation and the mean of the abundance of a\n", Rd_tag = "TEXT"), │ │ │ │ @@ -755,15 +755,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("ggplot2 object\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(DESeq2)\n", Rd_tag = "RCODE"), structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(humanGender)[idx,], design=~group)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeq(dds)\n", Rd_tag = "RCODE"), structure("res <- results(dds)\n", Rd_tag = "RCODE"), │ │ │ │ structure("degMV(colData(dds)[[\"group\"]],\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" res[, 4],\n", Rd_tag = "RCODE"), structure(" counts(dds, normalized = TRUE))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degMV.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" res[, 4],\n", Rd_tag = "RCODE"), structure(" counts(dds, normalized = TRUE))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degMV.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degMean (list) = structure(list(structure(list(structure("Distribution of pvalues by expression range", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degMean", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degMean", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function plot the p-values distribution colored by\n", Rd_tag = "TEXT"), │ │ │ │ structure("the quantiles of the average count data.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -777,15 +777,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("ggplot2 object\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(DESeq2)\n", Rd_tag = "RCODE"), structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(humanGender)[idx,], design=~group)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeq(dds)\n", Rd_tag = "RCODE"), structure("res <- results(dds)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("degMean(res[, 4], counts(dds))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degMean.Rd", class = "Rd", meta = list( │ │ │ │ + structure("degMean(res[, 4], counts(dds))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degMean.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degMerge (list) = structure(list(structure(list(structure("Integrate data comming from degPattern into one data object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degMerge", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degMerge", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The simplest case is if you want to conbine the pattern profile\n", Rd_tag = "TEXT"), │ │ │ │ structure("for gene expression data and proteomic data. It will use the first element\n", Rd_tag = "TEXT"), │ │ │ │ @@ -828,15 +828,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("mapping", Rd_tag = "TEXT")), │ │ │ │ list(structure("data.frame mapping table in case elements use\n", Rd_tag = "TEXT"), │ │ │ │ structure("different ID in the row.names of expression matrix. For instance,\n", Rd_tag = "TEXT"), │ │ │ │ structure("when integrating miRNA/mRNA.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A data.frame with information on what genes are in each cluster in\n", Rd_tag = "TEXT"), │ │ │ │ - structure("all data set, and the correlation value for each pair cluster comparison.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degMerge.Rd", class = "Rd", meta = list( │ │ │ │ + structure("all data set, and the correlation value for each pair cluster comparison.\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degMerge.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degObj (list) = structure(list(structure(list(structure("Create a deg object that can be used to plot expression values\n", Rd_tag = "TEXT"), │ │ │ │ structure("at shiny server:runGist(9930881)", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degObj", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degObj", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Create a deg object that can be used to plot expression values\n", Rd_tag = "TEXT"), │ │ │ │ @@ -850,15 +850,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("outfile", Rd_tag = "TEXT")), │ │ │ │ list(structure("File that will contain the object.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("R object to be load into vizExp.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(SummarizedExperiment)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("degObj(assays(humanGender)[[1]], colData(humanGender), NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degObj.Rd", class = "Rd", meta = list( │ │ │ │ + structure("degObj(assays(humanGender)[[1]], colData(humanGender), NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degObj.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degPCA (list) = structure(list(structure(list(structure("smart PCA from count matrix data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degPCA", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degPCA", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("nice plot using ggplot2 from prcomp function\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("degPCA(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -899,15 +899,15 @@ │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Lorena Pantano, Rory Kirchner, Michael Steinbaugh\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(DESeq2)\n", Rd_tag = "RCODE"), structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure("colData(humanGender)[idx,], design=~group)\n", Rd_tag = "RCODE"), │ │ │ │ structure("degPCA(log2(counts(dse)+0.5), colData(dse),\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" condition=\"group\", name=\"group\", shape=\"group\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degPCA.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" condition=\"group\", name=\"group\", shape=\"group\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degPCA.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degPatterns (list) = structure(list(structure(list(structure("Make groups of genes using expression profile.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degPatterns", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degPatterns", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Note that this function doesn't calculate significant\n", Rd_tag = "TEXT"), │ │ │ │ structure("difference between groups, so the\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1117,15 +1117,15 @@ │ │ │ │ structure("res <- degPatterns(ma, des, time=\"group\", col = \"other\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Use the data yourself for custom figures\n", Rd_tag = "RCODE"), │ │ │ │ structure(" ggplot(res[[\"normalized\"]],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" aes(group, value, color = other, fill = other)) +\n", Rd_tag = "RCODE"), │ │ │ │ structure(" geom_boxplot() +\n", Rd_tag = "RCODE"), │ │ │ │ structure(" geom_point(position = position_jitterdodge(dodge.width = 0.9)) +\n", Rd_tag = "RCODE"), │ │ │ │ structure(" # change the method to make it smoother\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" geom_smooth(aes(group=other), method = \"lm\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degPatterns.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" geom_smooth(aes(group=other), method = \"lm\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degPatterns.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degPlot (list) = structure(list(structure(list(structure("Plot top genes allowing more variables to color and shape points", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degPlot", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degPlot", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot top genes allowing more variables to color and shape points\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("degPlot(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -1219,15 +1219,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(DESeq2)\n", Rd_tag = "RCODE"), structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(humanGender)[idx,], design=~group)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dse <- DESeq(dse)\n", Rd_tag = "RCODE"), structure("degPlot(dse, genes = rownames(dse)[1:10], xs = \"group\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("degPlot(dse, genes = rownames(dse)[1:10], xs = \"group\", color = \"orange\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("degPlot(dse, genes = rownames(dse)[1:10], xs = \"group\", group = \"group\",\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" color = \"Accent\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degPlot.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" color = \"Accent\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degPlot.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degPlotCluster (list) = structure(list(structure(list(structure("Plot clusters from degPattern function output", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degPlotCluster", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degPlotCluster", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function helps to format the cluster plots from ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("degPatterns()", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("=degPatterns", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ @@ -1303,15 +1303,15 @@ │ │ │ │ structure("table <- rownames_to_column(as.data.frame(ma), \"genes\") %>%\n", Rd_tag = "RCODE"), │ │ │ │ structure(" gather(\"sample\", \"expression\", -genes) %>%\n", Rd_tag = "RCODE"), │ │ │ │ structure(" right_join(distinct(res$df[,c(\"genes\", \"cluster\")]),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" by = \"genes\") %>%\n", Rd_tag = "RCODE"), │ │ │ │ structure(" left_join(rownames_to_column(as.data.frame(des), \"sample\"),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" by = \"sample\") %>% \n", Rd_tag = "RCODE"), │ │ │ │ structure(" as.data.frame()\n", Rd_tag = "RCODE"), │ │ │ │ - structure("degPlotCluster(table, \"group\", \"other\", process = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degPlotCluster.Rd", class = "Rd", meta = list( │ │ │ │ + structure("degPlotCluster(table, \"group\", \"other\", process = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degPlotCluster.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degPlotWide (list) = structure(list(structure(list(structure("Plot selected genes on a wide format", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degPlotWide", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degPlotWide", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot selected genes on a wide format\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("degPlotWide(counts, genes, group, metadata = NULL, batch = NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1338,15 +1338,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("ggplot showing the expresison of the genes on the x\n", Rd_tag = "TEXT"), │ │ │ │ structure("axis\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(DESeq2)\n", Rd_tag = "RCODE"), structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(humanGender)[idx,], design=~group)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("dse <- DESeq(dse)\n", Rd_tag = "RCODE"), structure("degPlotWide(dse, rownames(dse)[1:10], group = \"group\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degPlotWide.Rd", class = "Rd", meta = list( │ │ │ │ + structure("dse <- DESeq(dse)\n", Rd_tag = "RCODE"), structure("degPlotWide(dse, rownames(dse)[1:10], group = \"group\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degPlotWide.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degQC (list) = structure(list(structure(list(structure("Plot main figures showing p-values distribution and mean-variance correlation", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degQC", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degQC", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function joins the output of ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("degMean", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("DEGreport", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ @@ -1373,15 +1373,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("ggplot2 object\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(DESeq2)\n", Rd_tag = "RCODE"), structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(humanGender)[idx,], design=~group)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeq(dds)\n", Rd_tag = "RCODE"), structure("res <- results(dds)\n", Rd_tag = "RCODE"), │ │ │ │ structure("degQC(counts(dds, normalized=TRUE), colData(dds)[[\"group\"]],\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" pvalue = res[[\"pvalue\"]])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degQC.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" pvalue = res[[\"pvalue\"]])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degQC.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degResults (list) = structure(list(structure(list(structure("Complete report from DESeq2 analysis", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degResults", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degResults", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Complete report from DESeq2 analysis\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("degResults(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -1440,15 +1440,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("ggplot2 object\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(DESeq2)\n", Rd_tag = "RCODE"), structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(humanGender)[idx,], design=~group)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dse <- DESeq(dse)\n", Rd_tag = "RCODE"), structure("res <- degResults(dds = dse, name = \"test\", org = NULL,\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" do_go = FALSE, group = \"group\", xs = \"group\", path_results = NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degResults.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" do_go = FALSE, group = \"group\", xs = \"group\", path_results = NULL)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degResults.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degSignature (list) = structure(list(structure(list(structure("Plot gene signature for each group and signature", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degSignature", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degSignature", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Given a list of genes beloging to a different classes, like\n", Rd_tag = "TEXT"), │ │ │ │ structure("markers, plot for each group, the expression values for all the samples.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1482,15 +1482,15 @@ │ │ │ │ list(structure("slotName in the case of SummarizedExperiment objects.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("scale", Rd_tag = "TEXT")), │ │ │ │ list(structure("Whether to scale or not the expression.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("ggplot plot.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("data(geneInfo)\n", Rd_tag = "RCODE"), structure("degSignature(humanGender, geneInfo, group = \"group\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degSignature.Rd", class = "Rd", meta = list( │ │ │ │ + structure("data(geneInfo)\n", Rd_tag = "RCODE"), structure("degSignature(humanGender, geneInfo, group = \"group\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degSignature.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degSummary (list) = structure(list(structure(list(structure("Print Summary Statistics of Alpha Level Cutoffs", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degSummary", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degSummary", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Print Summary Statistics of Alpha Level Cutoffs\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("degSummary(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -1540,15 +1540,15 @@ │ │ │ │ structure("dse <- DESeqDataSetFromMatrix(counts[1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(humanGender)[idx,],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" design = ~group)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dse <- DESeq(dse)\n", Rd_tag = "RCODE"), structure("res1 <- results(dse)\n", Rd_tag = "RCODE"), │ │ │ │ structure("res2 <- degComps(dse, contrast = c(\"group_Male_vs_Female\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("degSummary(dse, contrast = \"group_Male_vs_Female\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("degSummary(res1)\n", Rd_tag = "RCODE"), structure("degSummary(res1, kable = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("degSummary(res2[[1]])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degSummary.Rd", class = "Rd", meta = list( │ │ │ │ + structure("degSummary(res2[[1]])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degSummary.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degVB (list) = structure(list(structure(list(structure("Distribution of the standard desviation of\n", Rd_tag = "TEXT"), │ │ │ │ structure("DE genes compared to the background", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degVB", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degVB", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Distribution of the standard desviation of\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1571,15 +1571,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("ggplot2 object\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(DESeq2)\n", Rd_tag = "RCODE"), structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(humanGender)[idx,], design=~group)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeq(dds)\n", Rd_tag = "RCODE"), structure("res <- results(dds)\n", Rd_tag = "RCODE"), │ │ │ │ structure("degVB(row.names(res)[1:20], colData(dds)[[\"group\"]],\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" counts(dds, normalized = TRUE))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degVB.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" counts(dds, normalized = TRUE))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degVB.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degVar (list) = structure(list(structure(list(structure("Distribution of pvalues by standard desviation range", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degVar", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degVar", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function pot the p-valyes distribution colored by\n", Rd_tag = "TEXT"), │ │ │ │ structure("the quantiles of the standard desviation of count data.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1593,15 +1593,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("ggplot2 object\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(DESeq2)\n", Rd_tag = "RCODE"), structure("idx <- c(1:10, 75:85)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colData(humanGender)[idx,], design=~group)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeq(dds)\n", Rd_tag = "RCODE"), structure("res <- results(dds)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("degVar(res[, 4], counts(dds))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degVar.Rd", class = "Rd", meta = list( │ │ │ │ + structure("degVar(res[, 4], counts(dds))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degVar.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ degVolcano (list) = structure(list(structure(list(structure("Create volcano plot from log2FC and adjusted pvalues data frame", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("degVolcano", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("degVolcano", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Create volcano plot from log2FC and adjusted pvalues data frame\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("degVolcano(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -1657,25 +1657,25 @@ │ │ │ │ structure("with density of the fold change and p-values on the top and the\n", Rd_tag = "TEXT"), │ │ │ │ structure("right side of the volcano plot.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Lorena Pantano, John Hutchinson\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("library(DESeq2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- makeExampleDESeqDataSet(betaSD = 1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeq(dds)\n", Rd_tag = "RCODE"), structure("stats <- results(dds)[,c(\"log2FoldChange\", \"padj\")]\n", Rd_tag = "RCODE"), │ │ │ │ structure("stats[[\"name\"]] <- row.names(stats)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("degVolcano(stats, plot_text = stats[1:10,])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/degVolcano.Rd", class = "Rd", meta = list( │ │ │ │ + structure("degVolcano(stats, plot_text = stats[1:10,])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degVolcano.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ geneInfo (list) = structure(list(structure(list(structure("data.frame with chromose information for each gene", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("geneInfo", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("geneInfo", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("data.frame with chromose information for each gene\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(geneInfo)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("data.frame\n", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Lorena Pantano, 2014-08-14\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("biomart\n", Rd_tag = "TEXT")), Rd_tag = "\\source")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/geneInfo.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("biomart\n", Rd_tag = "TEXT")), Rd_tag = "\\source")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/geneInfo.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ geom_cor (list) = structure(list(structure(list(structure("Add correlation and p-value to a ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("ggplot2", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure(" plot", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("geom_cor", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("geom_cor", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1766,27 +1766,27 @@ │ │ │ │ structure(list(structure("ggplot2::layer()", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("ggplot2:layer", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(SummarizedExperiment)\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(ggplot2)\n", Rd_tag = "RCODE"), structure("ggplot(as.data.frame(assay(humanGender)[1:1000,]),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" aes(x = NA20502, y = NA20504)) +\n", Rd_tag = "RCODE"), │ │ │ │ structure(" geom_point() +\n", Rd_tag = "RCODE"), structure(" ylim(0,1.1e5) +\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" geom_cor(method = \"kendall\", ypos = 1e5) \n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/geom_cor.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" geom_cor(method = \"kendall\", ypos = 1e5) \n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/geom_cor.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ humanGender (list) = structure(list(structure(list(structure("DGEList object for DE genes betwen Male and Females", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("humanGender", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("humanGender", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("DGEList object for DE genes betwen Male and Females\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(humanGender)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("DGEList\n", Rd_tag = "TEXT")), Rd_tag = "\\format"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Lorena Pantano, 2017-08-37\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("gEUvadis\n", Rd_tag = "TEXT")), Rd_tag = "\\source")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/humanGender.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("gEUvadis\n", Rd_tag = "TEXT")), Rd_tag = "\\source")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/humanGender.Rd", class = "Rd", meta = list( │ │ │ │ docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -1873,10 +1873,10 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("library(DESeq2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- makeExampleDESeqDataSet(betaSD=1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("colData(dds)[[\"treatment\"]] <- sample(colData(dds)[[\"condition\"]], 12)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" design(dds) <- ~ condition + treatment\n", Rd_tag = "RCODE"), │ │ │ │ structure("dds <- DESeq(dds)\n", Rd_tag = "RCODE"), structure("res <- degComps(dds, contrast = list(\"treatment_B_vs_A\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" c(\"condition\", \"A\", \"B\")))\n", Rd_tag = "RCODE"), │ │ │ │ structure("significants(res, full = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# significants(res, full = TRUE, padj = 1) # all genes\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-degreport/man/significants.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# significants(res, full = TRUE, padj = 1) # all genes\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/significants.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/DEGreport/help/DEGreport.rdx │ │ │ ├── DEGreport.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,211 +1,211 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$DEGSet │ │ │ │ │ -[1] 283 3264 │ │ │ │ │ +[1] 293 3280 │ │ │ │ │ │ │ │ │ │ $variables$`DEGreport-deprecated` │ │ │ │ │ -[1] 3836 1885 │ │ │ │ │ +[1] 3874 1903 │ │ │ │ │ │ │ │ │ │ $variables$createReport │ │ │ │ │ -[1] 6003 1361 │ │ │ │ │ +[1] 6073 1378 │ │ │ │ │ │ │ │ │ │ $variables$deg │ │ │ │ │ -[1] 7641 1449 │ │ │ │ │ +[1] 7742 1466 │ │ │ │ │ │ │ │ │ │ $variables$degCheckFactors │ │ │ │ │ -[1] 9379 1730 │ │ │ │ │ +[1] 9508 1744 │ │ │ │ │ │ │ │ │ │ $variables$degColors │ │ │ │ │ -[1] 11392 2065 │ │ │ │ │ +[1] 11547 2079 │ │ │ │ │ │ │ │ │ │ $variables$degComps │ │ │ │ │ -[1] 13739 3254 │ │ │ │ │ +[1] 13920 3269 │ │ │ │ │ │ │ │ │ │ $variables$degCorCov │ │ │ │ │ -[1] 17277 1747 │ │ │ │ │ +[1] 17485 1762 │ │ │ │ │ │ │ │ │ │ $variables$degCovariates │ │ │ │ │ -[1] 19309 5011 │ │ │ │ │ +[1] 19545 5025 │ │ │ │ │ │ │ │ │ │ $variables$degDefault │ │ │ │ │ -[1] 24605 1507 │ │ │ │ │ +[1] 24866 1523 │ │ │ │ │ │ │ │ │ │ $variables$degFilter │ │ │ │ │ -[1] 26394 1780 │ │ │ │ │ +[1] 26684 1795 │ │ │ │ │ │ │ │ │ │ $variables$degMA │ │ │ │ │ -[1] 28455 1972 │ │ │ │ │ +[1] 28773 1987 │ │ │ │ │ │ │ │ │ │ $variables$degMB │ │ │ │ │ -[1] 30708 1444 │ │ │ │ │ +[1] 31054 1458 │ │ │ │ │ │ │ │ │ │ $variables$degMDS │ │ │ │ │ -[1] 32434 1510 │ │ │ │ │ +[1] 32806 1521 │ │ │ │ │ │ │ │ │ │ $variables$degMV │ │ │ │ │ -[1] 34225 1491 │ │ │ │ │ +[1] 34621 1505 │ │ │ │ │ │ │ │ │ │ $variables$degMean │ │ │ │ │ -[1] 35998 1215 │ │ │ │ │ +[1] 36420 1229 │ │ │ │ │ │ │ │ │ │ $variables$degMerge │ │ │ │ │ -[1] 37494 1981 │ │ │ │ │ +[1] 37943 1996 │ │ │ │ │ │ │ │ │ │ $variables$degObj │ │ │ │ │ -[1] 39756 1109 │ │ │ │ │ +[1] 40232 1125 │ │ │ │ │ │ │ │ │ │ $variables$degPCA │ │ │ │ │ -[1] 41148 1964 │ │ │ │ │ +[1] 41651 1979 │ │ │ │ │ │ │ │ │ │ $variables$degPatterns │ │ │ │ │ -[1] 43396 7144 │ │ │ │ │ +[1] 43926 7159 │ │ │ │ │ │ │ │ │ │ $variables$degPlot │ │ │ │ │ -[1] 50821 3455 │ │ │ │ │ +[1] 51379 3469 │ │ │ │ │ │ │ │ │ │ $variables$degPlotCluster │ │ │ │ │ -[1] 54563 3075 │ │ │ │ │ +[1] 55147 3090 │ │ │ │ │ │ │ │ │ │ $variables$degPlotWide │ │ │ │ │ -[1] 57922 1605 │ │ │ │ │ +[1] 58534 1622 │ │ │ │ │ │ │ │ │ │ $variables$degQC │ │ │ │ │ -[1] 59808 1706 │ │ │ │ │ +[1] 60449 1722 │ │ │ │ │ │ │ │ │ │ $variables$degResults │ │ │ │ │ -[1] 61797 2588 │ │ │ │ │ +[1] 62467 2603 │ │ │ │ │ │ │ │ │ │ $variables$degSignature │ │ │ │ │ -[1] 64669 1846 │ │ │ │ │ +[1] 65367 1862 │ │ │ │ │ │ │ │ │ │ $variables$degSummary │ │ │ │ │ -[1] 66799 2266 │ │ │ │ │ +[1] 67525 2280 │ │ │ │ │ │ │ │ │ │ $variables$degVB │ │ │ │ │ -[1] 69346 1467 │ │ │ │ │ +[1] 70098 1482 │ │ │ │ │ │ │ │ │ │ $variables$degVar │ │ │ │ │ -[1] 71094 1225 │ │ │ │ │ +[1] 71873 1239 │ │ │ │ │ │ │ │ │ │ $variables$degVolcano │ │ │ │ │ -[1] 72602 2302 │ │ │ │ │ +[1] 73407 2316 │ │ │ │ │ │ │ │ │ │ $variables$geneInfo │ │ │ │ │ -[1] 75185 703 │ │ │ │ │ +[1] 76017 717 │ │ │ │ │ │ │ │ │ │ $variables$geom_cor │ │ │ │ │ -[1] 76170 3800 │ │ │ │ │ +[1] 77028 3814 │ │ │ │ │ │ │ │ │ │ $variables$humanGender │ │ │ │ │ -[1] 80254 715 │ │ │ │ │ +[1] 81139 731 │ │ │ │ │ │ │ │ │ │ $variables$significants │ │ │ │ │ -[1] 81253 3076 │ │ │ │ │ +[1] 82167 3092 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 283 │ │ │ │ │ +[1] 0 293 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 24320 285 │ │ │ │ │ +[1] 24570 296 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 26112 282 │ │ │ │ │ +[1] 26389 295 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 28174 281 │ │ │ │ │ +[1] 28479 294 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 30427 281 │ │ │ │ │ +[1] 30760 294 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 32152 282 │ │ │ │ │ +[1] 32512 294 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 33944 281 │ │ │ │ │ +[1] 34327 294 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 35716 282 │ │ │ │ │ +[1] 36126 294 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 37213 281 │ │ │ │ │ +[1] 37649 294 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 39475 281 │ │ │ │ │ +[1] 39939 293 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 40865 283 │ │ │ │ │ +[1] 41357 294 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 3547 289 │ │ │ │ │ +[1] 3573 301 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 43112 284 │ │ │ │ │ +[1] 43630 296 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 50540 281 │ │ │ │ │ +[1] 51085 294 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 54276 287 │ │ │ │ │ +[1] 54848 299 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 57638 284 │ │ │ │ │ +[1] 58237 297 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 59527 281 │ │ │ │ │ +[1] 60156 293 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 61514 283 │ │ │ │ │ +[1] 62171 296 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ -[1] 64385 284 │ │ │ │ │ +[1] 65070 297 │ │ │ │ │ │ │ │ │ │ $references$`env::27` │ │ │ │ │ -[1] 66515 284 │ │ │ │ │ +[1] 67229 296 │ │ │ │ │ │ │ │ │ │ $references$`env::28` │ │ │ │ │ -[1] 69065 281 │ │ │ │ │ +[1] 69805 293 │ │ │ │ │ │ │ │ │ │ $references$`env::29` │ │ │ │ │ -[1] 70813 281 │ │ │ │ │ +[1] 71580 293 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 5721 282 │ │ │ │ │ +[1] 5777 296 │ │ │ │ │ │ │ │ │ │ $references$`env::30` │ │ │ │ │ -[1] 72319 283 │ │ │ │ │ +[1] 73112 295 │ │ │ │ │ │ │ │ │ │ $references$`env::31` │ │ │ │ │ -[1] 74904 281 │ │ │ │ │ +[1] 75723 294 │ │ │ │ │ │ │ │ │ │ $references$`env::32` │ │ │ │ │ -[1] 75888 282 │ │ │ │ │ +[1] 76734 294 │ │ │ │ │ │ │ │ │ │ $references$`env::33` │ │ │ │ │ -[1] 79970 284 │ │ │ │ │ +[1] 80842 297 │ │ │ │ │ │ │ │ │ │ $references$`env::34` │ │ │ │ │ -[1] 80969 284 │ │ │ │ │ +[1] 81870 297 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 7364 277 │ │ │ │ │ +[1] 7451 291 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 9090 289 │ │ │ │ │ +[1] 9208 300 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 11109 283 │ │ │ │ │ +[1] 11252 295 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 13457 282 │ │ │ │ │ +[1] 13626 294 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 16993 284 │ │ │ │ │ +[1] 17189 296 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 19024 285 │ │ │ │ │ +[1] 19247 298 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/DEGreport/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,36 +1,36 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-degreport/man/DEGSet.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-degreport/man/DEGreport-deprecated.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-degreport/man/createReport.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-degreport/man/deg.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-degreport/man/degCheckFactors.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-degreport/man/degColors.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-degreport/man/degComps.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-degreport/man/degCorCov.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-degreport/man/degCovariates.Rd" │ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-degreport/man/degDefault.Rd" │ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-degreport/man/degFilter.Rd" │ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-degreport/man/degMA.Rd" │ │ │ │ │ -[13] "/home/moeller/Salsa/r-bioc-degreport/man/degMB.Rd" │ │ │ │ │ -[14] "/home/moeller/Salsa/r-bioc-degreport/man/degMDS.Rd" │ │ │ │ │ -[15] "/home/moeller/Salsa/r-bioc-degreport/man/degMV.Rd" │ │ │ │ │ -[16] "/home/moeller/Salsa/r-bioc-degreport/man/degMean.Rd" │ │ │ │ │ -[17] "/home/moeller/Salsa/r-bioc-degreport/man/degMerge.Rd" │ │ │ │ │ -[18] "/home/moeller/Salsa/r-bioc-degreport/man/degObj.Rd" │ │ │ │ │ -[19] "/home/moeller/Salsa/r-bioc-degreport/man/degPCA.Rd" │ │ │ │ │ -[20] "/home/moeller/Salsa/r-bioc-degreport/man/degPatterns.Rd" │ │ │ │ │ -[21] "/home/moeller/Salsa/r-bioc-degreport/man/degPlot.Rd" │ │ │ │ │ -[22] "/home/moeller/Salsa/r-bioc-degreport/man/degPlotCluster.Rd" │ │ │ │ │ -[23] "/home/moeller/Salsa/r-bioc-degreport/man/degPlotWide.Rd" │ │ │ │ │ -[24] "/home/moeller/Salsa/r-bioc-degreport/man/degQC.Rd" │ │ │ │ │ -[25] "/home/moeller/Salsa/r-bioc-degreport/man/degResults.Rd" │ │ │ │ │ -[26] "/home/moeller/Salsa/r-bioc-degreport/man/degSignature.Rd" │ │ │ │ │ -[27] "/home/moeller/Salsa/r-bioc-degreport/man/degSummary.Rd" │ │ │ │ │ -[28] "/home/moeller/Salsa/r-bioc-degreport/man/degVB.Rd" │ │ │ │ │ -[29] "/home/moeller/Salsa/r-bioc-degreport/man/degVar.Rd" │ │ │ │ │ -[30] "/home/moeller/Salsa/r-bioc-degreport/man/degVolcano.Rd" │ │ │ │ │ -[31] "/home/moeller/Salsa/r-bioc-degreport/man/geneInfo.Rd" │ │ │ │ │ -[32] "/home/moeller/Salsa/r-bioc-degreport/man/geom_cor.Rd" │ │ │ │ │ -[33] "/home/moeller/Salsa/r-bioc-degreport/man/humanGender.Rd" │ │ │ │ │ -[34] "/home/moeller/Salsa/r-bioc-degreport/man/significants.Rd" │ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/DEGSet.Rd" │ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/DEGreport-deprecated.Rd" │ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/createReport.Rd" │ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/deg.Rd" │ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degCheckFactors.Rd" │ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degColors.Rd" │ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degComps.Rd" │ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degCorCov.Rd" │ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degCovariates.Rd" │ │ │ │ │ +[10] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degDefault.Rd" │ │ │ │ │ +[11] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degFilter.Rd" │ │ │ │ │ +[12] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degMA.Rd" │ │ │ │ │ +[13] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degMB.Rd" │ │ │ │ │ +[14] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degMDS.Rd" │ │ │ │ │ +[15] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degMV.Rd" │ │ │ │ │ +[16] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degMean.Rd" │ │ │ │ │ +[17] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degMerge.Rd" │ │ │ │ │ +[18] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degObj.Rd" │ │ │ │ │ +[19] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degPCA.Rd" │ │ │ │ │ +[20] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degPatterns.Rd" │ │ │ │ │ +[21] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degPlot.Rd" │ │ │ │ │ +[22] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degPlotCluster.Rd" │ │ │ │ │ +[23] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degPlotWide.Rd" │ │ │ │ │ +[24] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degQC.Rd" │ │ │ │ │ +[25] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degResults.Rd" │ │ │ │ │ +[26] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degSignature.Rd" │ │ │ │ │ +[27] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degSummary.Rd" │ │ │ │ │ +[28] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degVB.Rd" │ │ │ │ │ +[29] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degVar.Rd" │ │ │ │ │ +[30] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/degVolcano.Rd" │ │ │ │ │ +[31] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/geneInfo.Rd" │ │ │ │ │ +[32] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/geom_cor.Rd" │ │ │ │ │ +[33] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/humanGender.Rd" │ │ │ │ │ +[34] "/build/reproducible-path/r-bioc-degreport-1.48.0+dfsg/man/significants.Rd" │ │ │ │ │ attr(,"first") │ │ │ │ │ -[1] 42 │ │ │ │ │ +[1] 59