--- /srv/rebuilderd/tmp/rebuilderdcKSGvv/inputs/r-bioc-ballgown_2.43.0+dfsg-1_all.deb
+++ /srv/rebuilderd/tmp/rebuilderdcKSGvv/out/r-bioc-ballgown_2.43.0+dfsg-1_all.deb
├── file list
│ @@ -1,3 +1,3 @@
│  -rw-r--r--   0        0        0        4 2026-08-11 23:14:48.000000 debian-binary
│ --rw-r--r--   0        0        0     3092 2026-08-11 23:14:48.000000 control.tar.xz
│ --rw-r--r--   0        0        0  2918896 2026-08-11 23:14:48.000000 data.tar.xz
│ +-rw-r--r--   0        0        0     3088 2026-08-11 23:14:48.000000 control.tar.xz
│ +-rw-r--r--   0        0        0  2919760 2026-08-11 23:14:48.000000 data.tar.xz
├── control.tar.xz
│ ├── control.tar
│ │ ├── file list
│ │ │ @@ -1,3 +1,3 @@
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-11 23:14:48.000000 ./
│ │ │ --rw-r--r--   0 root         (0) root         (0)      877 2026-08-11 23:14:48.000000 ./control
│ │ │ +-rw-r--r--   0 root         (0) root         (0)      860 2026-08-11 23:14:48.000000 ./control
│ │ │  -rw-r--r--   0 root         (0) root         (0)    12285 2026-08-11 23:14:48.000000 ./md5sums
│ │ ├── ./control
│ │ │ @@ -1,14 +1,14 @@
│ │ │  Package: r-bioc-ballgown
│ │ │  Version: 2.43.0+dfsg-1
│ │ │  Architecture: all
│ │ │  Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
│ │ │ -Installed-Size: 4503
│ │ │ +Installed-Size: 4504
│ │ │  Depends: r-api-4.0, r-api-bioc-RELEASE, r-bioc-genomicranges (>= 1.17.25), r-bioc-iranges (>= 1.99.22), r-bioc-s4vectors (>= 0.9.39), r-cran-rcolorbrewer, r-bioc-sva, r-bioc-limma, r-bioc-rtracklayer (>= 1.29.25), r-bioc-biobase (>= 2.25.0), r-bioc-seqinfo, r-pkg-team-core-architecture
│ │ │ -Suggests: r-cran-testthat, r-cran-knitr, r-cran-markdown
│ │ │ +Suggests: r-cran-knitr, r-cran-markdown
│ │ │  Section: gnu-r
│ │ │  Priority: optional
│ │ │  Homepage: https://bioconductor.org/packages/ballgown/
│ │ │  Description: Flexible, isoform-level differential expression analysis
│ │ │   Tools for statistical analysis of assembled transcriptomes,
│ │ │   including flexible differential expression analysis, visualization of
│ │ │   transcript structures, and matching of assembled transcripts to annotation.
│ │ ├── ./md5sums
│ │ │ ├── ./md5sums
│ │ │ │┄ Files differ
├── data.tar.xz
│ ├── data.tar
│ │ ├── file list
│ │ │ @@ -15,22 +15,22 @@
│ │ │  -rw-r--r--   0 root         (0) root         (0)      655 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/Meta/nsInfo.rds
│ │ │  -rw-r--r--   0 root         (0) root         (0)     1477 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/Meta/package.rds
│ │ │  -rw-r--r--   0 root         (0) root         (0)      254 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/Meta/vignette.rds
│ │ │  -rw-r--r--   0 root         (0) root         (0)     1599 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/NAMESPACE
│ │ │  -rw-r--r--   0 root         (0) root         (0)     2338 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/NEWS
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/R/
│ │ │  -rw-r--r--   0 root         (0) root         (0)     1058 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/R/ballgown
│ │ │ --rw-r--r--   0 root         (0) root         (0)   464670 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/R/ballgown.rdb
│ │ │ --rw-r--r--   0 root         (0) root         (0)     2055 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/R/ballgown.rdx
│ │ │ +-rw-r--r--   0 root         (0) root         (0)   464682 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/R/ballgown.rdb
│ │ │ +-rw-r--r--   0 root         (0) root         (0)     2049 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/R/ballgown.rdx
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/data/
│ │ │  -rw-r--r--   0 root         (0) root         (0)   253876 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/data/bg.rda
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/doc/
│ │ │  -rw-r--r--   0 root         (0) root         (0)     4309 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/doc/ballgown.R
│ │ │  -rw-r--r--   0 root         (0) root         (0)    24854 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/doc/ballgown.Rmd
│ │ │ --rw-r--r--   0 root         (0) root         (0)    38813 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/doc/ballgown.html
│ │ │ +-rw-r--r--   0 root         (0) root         (0)    38451 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/doc/ballgown.html
│ │ │  -rw-r--r--   0 root         (0) root         (0)     1425 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/doc/index.html
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/extdata/
│ │ │  -rw-r--r--   0 root         (0) root         (0)   152184 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/extdata/annot.gtf.gz
│ │ │  -rw-r--r--   0 root         (0) root         (0)    68562 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/extdata/hg19_genes_small.gtf.gz
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/extdata/sample01/
│ │ │  -rw-r--r--   0 root         (0) root         (0)     6173 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/extdata/sample01/e2t.ctab
│ │ │  -rw-r--r--   0 root         (0) root         (0)    42711 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/extdata/sample01/e_data.ctab
│ │ │ @@ -154,17 +154,17 @@
│ │ │  -rw-r--r--   0 root         (0) root         (0)   383664 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/extdata/tiny.genes.results.gz
│ │ │  -rw-r--r--   0 root         (0) root         (0)   468320 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/extdata/tiny.isoforms.results.gz
│ │ │  -rw-r--r--   0 root         (0) root         (0)   383653 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/extdata/tiny2.genes.results.gz
│ │ │  -rw-r--r--   0 root         (0) root         (0)   467983 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/extdata/tiny2.isoforms.results.gz
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/help/
│ │ │  -rw-r--r--   0 root         (0) root         (0)     1717 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/help/AnIndex
│ │ │  -rw-r--r--   0 root         (0) root         (0)      619 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/help/aliases.rds
│ │ │ --rw-r--r--   0 root         (0) root         (0)    92857 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/help/ballgown.rdb
│ │ │ --rw-r--r--   0 root         (0) root         (0)     1109 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/help/ballgown.rdx
│ │ │ --rw-r--r--   0 root         (0) root         (0)      502 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/help/paths.rds
│ │ │ +-rw-r--r--   0 root         (0) root         (0)    93936 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/help/ballgown.rdb
│ │ │ +-rw-r--r--   0 root         (0) root         (0)     1106 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/help/ballgown.rdx
│ │ │ +-rw-r--r--   0 root         (0) root         (0)      517 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/help/paths.rds
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/html/
│ │ │  -rw-r--r--   0 root         (0) root         (0)    10323 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/html/00Index.html
│ │ │  -rw-r--r--   0 root         (0) root         (0)     2133 2026-08-11 23:14:48.000000 ./usr/lib/R/site-library/ballgown/html/R.css
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-11 23:14:48.000000 ./usr/share/
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-11 23:14:48.000000 ./usr/share/doc/
│ │ │  drwxr-xr-x   0 root         (0) root         (0)        0 2026-08-11 23:14:48.000000 ./usr/share/doc/r-bioc-ballgown/
│ │ │  -rw-r--r--   0 root         (0) root         (0)      982 2026-08-11 23:14:48.000000 ./usr/share/doc/r-bioc-ballgown/changelog.Debian.gz
│ │ ├── ./usr/lib/R/site-library/ballgown/R/ballgown.rdb
│ │ │ ├── Rscript --vanilla - {}
│ │ │ │ @@ -703,15 +703,15 @@
│ │ │ │      "imports" = "asVector = "asVector", spline.des = "spline.des", backSpline = "backSpline", "
│ │ │ │      "imports" = "ns = "ns", xyVector = "xyVector", periodicSpline = "periodicSpline", "
│ │ │ │      "imports" = "splineOrder = "splineOrder", polySpline = "polySpline"), Biobase = c("pData<-" = "pData<-"), "
│ │ │ │      "imports" = "    Biobase = c(pData = "pData"), Biobase = c(sampleNames = "sampleNames"), "
│ │ │ │      "imports" = "    Seqinfo = c(seqnames = "seqnames"), limma = c(lmFit = "lmFit"), "
│ │ │ │      "imports" = "    rtracklayer = c(import = "import"), sva = c(f.pvalue = "f.pvalue"))"
│ │ │ │      "lazydata" = "<environment>"
│ │ │ │ -    "path" = ""/home/moeller/Salsa/r-bioc-ballgown/debian/r-bioc-ballgown/usr/lib/R/site-library/ballgown""
│ │ │ │ +    "path" = ""/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/debian/r-bioc-ballgown/usr/lib/R/site-library/ballgown""
│ │ │ │      "spec" = "c(name = "ballgown", version = "2.43.0")"
│ │ │ │  }
│ │ │ │  
│ │ │ │  .__S3MethodsTable__. (environment) = 
│ │ │ │  {
│ │ │ │  }
│ │ ├── ./usr/lib/R/site-library/ballgown/R/ballgown.rdx
│ │ │ ├── ballgown.rdx-content
│ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}
│ │ │ │ │ @@ -1,565 +1,565 @@
│ │ │ │ │  $variables
│ │ │ │ │  $variables$.__C__ballgown
│ │ │ │ │  [1]   0 357
│ │ │ │ │  
│ │ │ │ │  $variables$.__NAMESPACE__.
│ │ │ │ │ -[1] 10949    52
│ │ │ │ │ +[1] 10961    52
│ │ │ │ │  
│ │ │ │ │  $variables$.__S3MethodsTable__.
│ │ │ │ │ -[1] 11132    52
│ │ │ │ │ +[1] 11144    52
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__dirs:ballgown`
│ │ │ │ │ -[1] 12480    52
│ │ │ │ │ +[1] 12492    52
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__eexpr:ballgown`
│ │ │ │ │ -[1] 19549    52
│ │ │ │ │ +[1] 19561    52
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__expr:ballgown`
│ │ │ │ │ -[1] 20904    53
│ │ │ │ │ +[1] 20916    53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__expr<-:ballgown`
│ │ │ │ │ -[1] 22656    53
│ │ │ │ │ +[1] 22668    53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__geneIDs:ballgown`
│ │ │ │ │ -[1] 24773    53
│ │ │ │ │ +[1] 24785    53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__geneNames:ballgown`
│ │ │ │ │ -[1] 26903    53
│ │ │ │ │ +[1] 26915    53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__gexpr:ballgown`
│ │ │ │ │ -[1] 34934    53
│ │ │ │ │ +[1] 34946    53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__iexpr:ballgown`
│ │ │ │ │ -[1] 41731    53
│ │ │ │ │ +[1] 41743    53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__indexes:ballgown`
│ │ │ │ │ -[1] 43095    53
│ │ │ │ │ +[1] 43107    53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__indexes<-:ballgown`
│ │ │ │ │ -[1] 44845    53
│ │ │ │ │ +[1] 44857    53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__mergedDate:ballgown`
│ │ │ │ │ -[1] 46220    53
│ │ │ │ │ +[1] 46232    53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__pData:Biobase`
│ │ │ │ │ -[1] 48420    53
│ │ │ │ │ +[1] 48432    53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__pData<-:Biobase`
│ │ │ │ │ -[1] 52988    53
│ │ │ │ │ +[1] 53000    53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__sampleNames:Biobase`
│ │ │ │ │ -[1] 59992    53
│ │ │ │ │ +[1] 60004    53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__seqnames:Seqinfo`
│ │ │ │ │ -[1] 66481    53
│ │ │ │ │ +[1] 66493    53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__show:methods`
│ │ │ │ │ -[1] 326677     53
│ │ │ │ │ +[1] 326689     53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__structure:ballgown`
│ │ │ │ │ -[1] 328045     53
│ │ │ │ │ +[1] 328057     53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__subset:base`
│ │ │ │ │ -[1] 341852     53
│ │ │ │ │ +[1] 341864     53
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__texpr:ballgown`
│ │ │ │ │ -[1] 348766     54
│ │ │ │ │ +[1] 348778     54
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__transcriptIDs:ballgown`
│ │ │ │ │ -[1] 350493     54
│ │ │ │ │ +[1] 350505     54
│ │ │ │ │  
│ │ │ │ │  $variables$`.__T__transcriptNames:ballgown`
│ │ │ │ │ -[1] 352649     54
│ │ │ │ │ +[1] 352661     54
│ │ │ │ │  
│ │ │ │ │  $variables$.makepretty
│ │ │ │ │ -[1] 352703    341
│ │ │ │ │ +[1] 352715    341
│ │ │ │ │  
│ │ │ │ │  $variables$.packageName
│ │ │ │ │ -[1] 353044     53
│ │ │ │ │ +[1] 353056     53
│ │ │ │ │  
│ │ │ │ │  $variables$.readExon
│ │ │ │ │ -[1] 353097   1278
│ │ │ │ │ +[1] 353109   1278
│ │ │ │ │  
│ │ │ │ │  $variables$.readIntron
│ │ │ │ │ -[1] 354375   1190
│ │ │ │ │ +[1] 354387   1190
│ │ │ │ │  
│ │ │ │ │  $variables$.readTranscript
│ │ │ │ │ -[1] 355565   1239
│ │ │ │ │ +[1] 355577   1239
│ │ │ │ │  
│ │ │ │ │  $variables$annotate_assembly
│ │ │ │ │ -[1] 356804   2251
│ │ │ │ │ +[1] 356816   2251
│ │ │ │ │  
│ │ │ │ │  $variables$assessSim
│ │ │ │ │ -[1] 359055   8287
│ │ │ │ │ +[1] 359067   8287
│ │ │ │ │  
│ │ │ │ │  $variables$ballgown
│ │ │ │ │ -[1] 367342  13066
│ │ │ │ │ +[1] 367354  13066
│ │ │ │ │  
│ │ │ │ │  $variables$ballgownrsem
│ │ │ │ │ -[1] 380408  11035
│ │ │ │ │ +[1] 380420  11035
│ │ │ │ │  
│ │ │ │ │  $variables$checkAssembledTx
│ │ │ │ │ -[1] 391443   5834
│ │ │ │ │ +[1] 391455   5834
│ │ │ │ │  
│ │ │ │ │  $variables$closestColor
│ │ │ │ │ -[1] 397277    507
│ │ │ │ │ +[1] 397289    507
│ │ │ │ │  
│ │ │ │ │  $variables$clusterTranscripts
│ │ │ │ │ -[1] 397784   2990
│ │ │ │ │ +[1] 397796   2990
│ │ │ │ │  
│ │ │ │ │  $variables$collapseTranscripts
│ │ │ │ │ -[1] 400774   4152
│ │ │ │ │ +[1] 400786   4152
│ │ │ │ │  
│ │ │ │ │  $variables$contains
│ │ │ │ │ -[1] 404926   2493
│ │ │ │ │ +[1] 404938   2493
│ │ │ │ │  
│ │ │ │ │  $variables$dirs
│ │ │ │ │ -[1] 407419    392
│ │ │ │ │ +[1] 407431    392
│ │ │ │ │  
│ │ │ │ │  $variables$eexpr
│ │ │ │ │ -[1] 407811    421
│ │ │ │ │ +[1] 407823    421
│ │ │ │ │  
│ │ │ │ │  $variables$expr
│ │ │ │ │ -[1] 408232    394
│ │ │ │ │ +[1] 408244    394
│ │ │ │ │  
│ │ │ │ │  $variables$`expr<-`
│ │ │ │ │ -[1] 408626    417
│ │ │ │ │ +[1] 408638    417
│ │ │ │ │  
│ │ │ │ │  $variables$exprfilter
│ │ │ │ │ -[1] 409043   2966
│ │ │ │ │ +[1] 409055   2966
│ │ │ │ │  
│ │ │ │ │  $variables$geneIDs
│ │ │ │ │ -[1] 412009    394
│ │ │ │ │ +[1] 412021    394
│ │ │ │ │  
│ │ │ │ │  $variables$geneNames
│ │ │ │ │ -[1] 412403    398
│ │ │ │ │ +[1] 412415    398
│ │ │ │ │  
│ │ │ │ │  $variables$getAttributeField
│ │ │ │ │ -[1] 412801    923
│ │ │ │ │ +[1] 412813    923
│ │ │ │ │  
│ │ │ │ │  $variables$getGenes
│ │ │ │ │ -[1] 413724   1783
│ │ │ │ │ +[1] 413736   1783
│ │ │ │ │  
│ │ │ │ │  $variables$gexpr
│ │ │ │ │ -[1] 415507    395
│ │ │ │ │ +[1] 415519    395
│ │ │ │ │  
│ │ │ │ │  $variables$gffRead
│ │ │ │ │ -[1] 415902   1296
│ │ │ │ │ +[1] 415914   1296
│ │ │ │ │  
│ │ │ │ │  $variables$gffReadGR
│ │ │ │ │ -[1] 417198    898
│ │ │ │ │ +[1] 417210    898
│ │ │ │ │  
│ │ │ │ │  $variables$half2
│ │ │ │ │ -[1] 418096    290
│ │ │ │ │ +[1] 418108    290
│ │ │ │ │  
│ │ │ │ │  $variables$iexpr
│ │ │ │ │ -[1] 418386    423
│ │ │ │ │ +[1] 418398    423
│ │ │ │ │  
│ │ │ │ │  $variables$indexes
│ │ │ │ │ -[1] 418809    394
│ │ │ │ │ +[1] 418821    394
│ │ │ │ │  
│ │ │ │ │  $variables$`indexes<-`
│ │ │ │ │ -[1] 419203    421
│ │ │ │ │ +[1] 419215    421
│ │ │ │ │  
│ │ │ │ │  $variables$last
│ │ │ │ │ -[1] 419624    253
│ │ │ │ │ +[1] 419636    253
│ │ │ │ │  
│ │ │ │ │  $variables$match.data.frame
│ │ │ │ │ -[1] 419877    379
│ │ │ │ │ +[1] 419889    379
│ │ │ │ │  
│ │ │ │ │  $variables$mergedDate
│ │ │ │ │ -[1] 420256    399
│ │ │ │ │ +[1] 420268    399
│ │ │ │ │  
│ │ │ │ │  $variables$pData
│ │ │ │ │ -[1] 420655    495
│ │ │ │ │ +[1] 420667    495
│ │ │ │ │  
│ │ │ │ │  $variables$`pData<-`
│ │ │ │ │ -[1] 421150    516
│ │ │ │ │ +[1] 421162    516
│ │ │ │ │  
│ │ │ │ │  $variables$pctOverlap
│ │ │ │ │ -[1] 421666   1884
│ │ │ │ │ +[1] 421678   1884
│ │ │ │ │  
│ │ │ │ │  $variables$plotLatentTranscripts
│ │ │ │ │ -[1] 423550   2727
│ │ │ │ │ +[1] 423562   2727
│ │ │ │ │  
│ │ │ │ │  $variables$plotMeans
│ │ │ │ │ -[1] 426277   9207
│ │ │ │ │ +[1] 426289   9207
│ │ │ │ │  
│ │ │ │ │  $variables$plotTranscripts
│ │ │ │ │ -[1] 435484  12205
│ │ │ │ │ +[1] 435496  12205
│ │ │ │ │  
│ │ │ │ │  $variables$sampleNames
│ │ │ │ │ -[1] 447689    499
│ │ │ │ │ +[1] 447701    499
│ │ │ │ │  
│ │ │ │ │  $variables$seqnames
│ │ │ │ │ -[1] 448188    494
│ │ │ │ │ +[1] 448200    494
│ │ │ │ │  
│ │ │ │ │  $variables$ss
│ │ │ │ │ -[1] 448682    331
│ │ │ │ │ +[1] 448694    331
│ │ │ │ │  
│ │ │ │ │  $variables$stattest
│ │ │ │ │ -[1] 449013   9032
│ │ │ │ │ +[1] 449025   9032
│ │ │ │ │  
│ │ │ │ │  $variables$strip_quotes
│ │ │ │ │ -[1] 458045    305
│ │ │ │ │ +[1] 458057    305
│ │ │ │ │  
│ │ │ │ │  $variables$structure
│ │ │ │ │ -[1] 458350    402
│ │ │ │ │ +[1] 458362    402
│ │ │ │ │  
│ │ │ │ │  $variables$subset
│ │ │ │ │ -[1] 458752    433
│ │ │ │ │ +[1] 458764    433
│ │ │ │ │  
│ │ │ │ │  $variables$tGene
│ │ │ │ │ -[1] 459185   1367
│ │ │ │ │ +[1] 459197   1367
│ │ │ │ │  
│ │ │ │ │  $variables$texpr
│ │ │ │ │ -[1] 460552    423
│ │ │ │ │ +[1] 460564    423
│ │ │ │ │  
│ │ │ │ │  $variables$transcriptIDs
│ │ │ │ │ -[1] 460975    404
│ │ │ │ │ +[1] 460987    404
│ │ │ │ │  
│ │ │ │ │  $variables$transcriptNames
│ │ │ │ │ -[1] 461379    405
│ │ │ │ │ +[1] 461391    405
│ │ │ │ │  
│ │ │ │ │  $variables$writeFiles
│ │ │ │ │ -[1] 461784   2886
│ │ │ │ │ +[1] 461796   2886
│ │ │ │ │  
│ │ │ │ │  
│ │ │ │ │  $references
│ │ │ │ │  $references$`env::1`
│ │ │ │ │ -[1]   646 10303
│ │ │ │ │ +[1]   646 10315
│ │ │ │ │  
│ │ │ │ │  $references$`env::10`
│ │ │ │ │ -[1] 17038   258
│ │ │ │ │ +[1] 17050   258
│ │ │ │ │  
│ │ │ │ │  $references$`env::100`
│ │ │ │ │ -[1] 346566   2200
│ │ │ │ │ +[1] 346578   2200
│ │ │ │ │  
│ │ │ │ │  $references$`env::101`
│ │ │ │ │ -[1] 346305    261
│ │ │ │ │ +[1] 346317    261
│ │ │ │ │  
│ │ │ │ │  $references$`env::102`
│ │ │ │ │ -[1] 341905   2200
│ │ │ │ │ +[1] 341917   2200
│ │ │ │ │  
│ │ │ │ │  $references$`env::103`
│ │ │ │ │ -[1] 344105   2200
│ │ │ │ │ +[1] 344117   2200
│ │ │ │ │  
│ │ │ │ │  $references$`env::104`
│ │ │ │ │ -[1] 350023    470
│ │ │ │ │ +[1] 350035    470
│ │ │ │ │  
│ │ │ │ │  $references$`env::105`
│ │ │ │ │ -[1] 349760    263
│ │ │ │ │ +[1] 349772    263
│ │ │ │ │  
│ │ │ │ │  $references$`env::106`
│ │ │ │ │ -[1] 348820    470
│ │ │ │ │ +[1] 348832    470
│ │ │ │ │  
│ │ │ │ │  $references$`env::107`
│ │ │ │ │ -[1] 349290    470
│ │ │ │ │ +[1] 349302    470
│ │ │ │ │  
│ │ │ │ │  $references$`env::108`
│ │ │ │ │ -[1] 352036    613
│ │ │ │ │ +[1] 352048    613
│ │ │ │ │  
│ │ │ │ │  $references$`env::109`
│ │ │ │ │ -[1] 351773    263
│ │ │ │ │ +[1] 351785    263
│ │ │ │ │  
│ │ │ │ │  $references$`env::11`
│ │ │ │ │ -[1] 12532  2253
│ │ │ │ │ +[1] 12544  2253
│ │ │ │ │  
│ │ │ │ │  $references$`env::110`
│ │ │ │ │ -[1] 350547    613
│ │ │ │ │ +[1] 350559    613
│ │ │ │ │  
│ │ │ │ │  $references$`env::111`
│ │ │ │ │ -[1] 351160    613
│ │ │ │ │ +[1] 351172    613
│ │ │ │ │  
│ │ │ │ │  $references$`env::12`
│ │ │ │ │ -[1] 14785  2253
│ │ │ │ │ +[1] 14797  2253
│ │ │ │ │  
│ │ │ │ │  $references$`env::13`
│ │ │ │ │ -[1] 20555   349
│ │ │ │ │ +[1] 20567   349
│ │ │ │ │  
│ │ │ │ │  $references$`env::14`
│ │ │ │ │ -[1] 20299   256
│ │ │ │ │ +[1] 20311   256
│ │ │ │ │  
│ │ │ │ │  $references$`env::15`
│ │ │ │ │ -[1] 19601   349
│ │ │ │ │ +[1] 19613   349
│ │ │ │ │  
│ │ │ │ │  $references$`env::16`
│ │ │ │ │ -[1] 19950   349
│ │ │ │ │ +[1] 19962   349
│ │ │ │ │  
│ │ │ │ │  $references$`env::17`
│ │ │ │ │ -[1] 22177   479
│ │ │ │ │ +[1] 22189   479
│ │ │ │ │  
│ │ │ │ │  $references$`env::18`
│ │ │ │ │ -[1] 21915   262
│ │ │ │ │ +[1] 21927   262
│ │ │ │ │  
│ │ │ │ │  $references$`env::19`
│ │ │ │ │ -[1] 20957   479
│ │ │ │ │ +[1] 20969   479
│ │ │ │ │  
│ │ │ │ │  $references$`env::2`
│ │ │ │ │  [1] 357 131
│ │ │ │ │  
│ │ │ │ │  $references$`env::20`
│ │ │ │ │ -[1] 21436   479
│ │ │ │ │ +[1] 21448   479
│ │ │ │ │  
│ │ │ │ │  $references$`env::21`
│ │ │ │ │ -[1] 24171   602
│ │ │ │ │ +[1] 24183   602
│ │ │ │ │  
│ │ │ │ │  $references$`env::22`
│ │ │ │ │ -[1] 23913   258
│ │ │ │ │ +[1] 23925   258
│ │ │ │ │  
│ │ │ │ │  $references$`env::23`
│ │ │ │ │ -[1] 22709   602
│ │ │ │ │ +[1] 22721   602
│ │ │ │ │  
│ │ │ │ │  $references$`env::24`
│ │ │ │ │ -[1] 23311   602
│ │ │ │ │ +[1] 23323   602
│ │ │ │ │  
│ │ │ │ │  $references$`env::25`
│ │ │ │ │ -[1] 26297   606
│ │ │ │ │ +[1] 26309   606
│ │ │ │ │  
│ │ │ │ │  $references$`env::26`
│ │ │ │ │ -[1] 26038   259
│ │ │ │ │ +[1] 26050   259
│ │ │ │ │  
│ │ │ │ │  $references$`env::27`
│ │ │ │ │ -[1] 24826   606
│ │ │ │ │ +[1] 24838   606
│ │ │ │ │  
│ │ │ │ │  $references$`env::28`
│ │ │ │ │ -[1] 25432   606
│ │ │ │ │ +[1] 25444   606
│ │ │ │ │  
│ │ │ │ │  $references$`env::29`
│ │ │ │ │ -[1] 32360  2574
│ │ │ │ │ +[1] 32372  2574
│ │ │ │ │  
│ │ │ │ │  $references$`env::3`
│ │ │ │ │  [1] 488 158
│ │ │ │ │  
│ │ │ │ │  $references$`env::30`
│ │ │ │ │ -[1] 32104   256
│ │ │ │ │ +[1] 32116   256
│ │ │ │ │  
│ │ │ │ │  $references$`env::31`
│ │ │ │ │ -[1] 26956  2574
│ │ │ │ │ +[1] 26968  2574
│ │ │ │ │  
│ │ │ │ │  $references$`env::32`
│ │ │ │ │ -[1] 29530  2574
│ │ │ │ │ +[1] 29542  2574
│ │ │ │ │  
│ │ │ │ │  $references$`env::33`
│ │ │ │ │ -[1] 39569  2162
│ │ │ │ │ +[1] 39581  2162
│ │ │ │ │  
│ │ │ │ │  $references$`env::34`
│ │ │ │ │ -[1] 39311   258
│ │ │ │ │ +[1] 39323   258
│ │ │ │ │  
│ │ │ │ │  $references$`env::35`
│ │ │ │ │ -[1] 34987  2162
│ │ │ │ │ +[1] 34999  2162
│ │ │ │ │  
│ │ │ │ │  $references$`env::36`
│ │ │ │ │ -[1] 37149  2162
│ │ │ │ │ +[1] 37161  2162
│ │ │ │ │  
│ │ │ │ │  $references$`env::37`
│ │ │ │ │ -[1] 42744   351
│ │ │ │ │ +[1] 42756   351
│ │ │ │ │  
│ │ │ │ │  $references$`env::38`
│ │ │ │ │ -[1] 42486   258
│ │ │ │ │ +[1] 42498   258
│ │ │ │ │  
│ │ │ │ │  $references$`env::39`
│ │ │ │ │ -[1] 41784   351
│ │ │ │ │ +[1] 41796   351
│ │ │ │ │  
│ │ │ │ │  $references$`env::4`
│ │ │ │ │ -[1] 11001   131
│ │ │ │ │ +[1] 11013   131
│ │ │ │ │  
│ │ │ │ │  $references$`env::40`
│ │ │ │ │ -[1] 42135   351
│ │ │ │ │ +[1] 42147   351
│ │ │ │ │  
│ │ │ │ │  $references$`env::41`
│ │ │ │ │ -[1] 44367   478
│ │ │ │ │ +[1] 44379   478
│ │ │ │ │  
│ │ │ │ │  $references$`env::42`
│ │ │ │ │ -[1] 44104   263
│ │ │ │ │ +[1] 44116   263
│ │ │ │ │  
│ │ │ │ │  $references$`env::43`
│ │ │ │ │ -[1] 43148   478
│ │ │ │ │ +[1] 43160   478
│ │ │ │ │  
│ │ │ │ │  $references$`env::44`
│ │ │ │ │ -[1] 43626   478
│ │ │ │ │ +[1] 43638   478
│ │ │ │ │  
│ │ │ │ │  $references$`env::45`
│ │ │ │ │ -[1] 45866   354
│ │ │ │ │ +[1] 45878   354
│ │ │ │ │  
│ │ │ │ │  $references$`env::46`
│ │ │ │ │ -[1] 45606   260
│ │ │ │ │ +[1] 45618   260
│ │ │ │ │  
│ │ │ │ │  $references$`env::47`
│ │ │ │ │ -[1] 44898   354
│ │ │ │ │ +[1] 44910   354
│ │ │ │ │  
│ │ │ │ │  $references$`env::48`
│ │ │ │ │ -[1] 45252   354
│ │ │ │ │ +[1] 45264   354
│ │ │ │ │  
│ │ │ │ │  $references$`env::49`
│ │ │ │ │ -[1] 47790   630
│ │ │ │ │ +[1] 47802   630
│ │ │ │ │  
│ │ │ │ │  $references$`env::5`
│ │ │ │ │ -[1] 12133   347
│ │ │ │ │ +[1] 12145   347
│ │ │ │ │  
│ │ │ │ │  $references$`env::50`
│ │ │ │ │ -[1] 47533   257
│ │ │ │ │ +[1] 47545   257
│ │ │ │ │  
│ │ │ │ │  $references$`env::51`
│ │ │ │ │ -[1] 46273   630
│ │ │ │ │ +[1] 46285   630
│ │ │ │ │  
│ │ │ │ │  $references$`env::52`
│ │ │ │ │ -[1] 46903   630
│ │ │ │ │ +[1] 46915   630
│ │ │ │ │  
│ │ │ │ │  $references$`env::53`
│ │ │ │ │ -[1] 51569  1419
│ │ │ │ │ +[1] 51581  1419
│ │ │ │ │  
│ │ │ │ │  $references$`env::54`
│ │ │ │ │ -[1] 51311   258
│ │ │ │ │ +[1] 51323   258
│ │ │ │ │  
│ │ │ │ │  $references$`env::55`
│ │ │ │ │ -[1] 48473  1419
│ │ │ │ │ +[1] 48485  1419
│ │ │ │ │  
│ │ │ │ │  $references$`env::56`
│ │ │ │ │ -[1] 49892  1419
│ │ │ │ │ +[1] 49904  1419
│ │ │ │ │  
│ │ │ │ │  $references$`env::57`
│ │ │ │ │ -[1] 57763  2229
│ │ │ │ │ +[1] 57775  2229
│ │ │ │ │  
│ │ │ │ │  $references$`env::58`
│ │ │ │ │ -[1] 57499   264
│ │ │ │ │ +[1] 57511   264
│ │ │ │ │  
│ │ │ │ │  $references$`env::59`
│ │ │ │ │ -[1] 53041  2229
│ │ │ │ │ +[1] 53053  2229
│ │ │ │ │  
│ │ │ │ │  $references$`env::6`
│ │ │ │ │ -[1] 11878   255
│ │ │ │ │ +[1] 11890   255
│ │ │ │ │  
│ │ │ │ │  $references$`env::60`
│ │ │ │ │ -[1] 55270  2229
│ │ │ │ │ +[1] 55282  2229
│ │ │ │ │  
│ │ │ │ │  $references$`env::61`
│ │ │ │ │ -[1] 64421  2060
│ │ │ │ │ +[1] 64433  2060
│ │ │ │ │  
│ │ │ │ │  $references$`env::62`
│ │ │ │ │ -[1] 64165   256
│ │ │ │ │ +[1] 64177   256
│ │ │ │ │  
│ │ │ │ │  $references$`env::63`
│ │ │ │ │ -[1] 60045  2060
│ │ │ │ │ +[1] 60057  2060
│ │ │ │ │  
│ │ │ │ │  $references$`env::64`
│ │ │ │ │ -[1] 62105  2060
│ │ │ │ │ +[1] 62117  2060
│ │ │ │ │  
│ │ │ │ │  $references$`env::65`
│ │ │ │ │ -[1] 326041    636
│ │ │ │ │ +[1] 326053    636
│ │ │ │ │  
│ │ │ │ │  $references$`env::66`
│ │ │ │ │ -[1] 325582    459
│ │ │ │ │ +[1] 325594    459
│ │ │ │ │  
│ │ │ │ │  $references$`env::67`
│ │ │ │ │ -[1] 208134  58724
│ │ │ │ │ +[1] 208146  58724
│ │ │ │ │  
│ │ │ │ │  $references$`env::68`
│ │ │ │ │ -[1] 66534   170
│ │ │ │ │ +[1] 66546   170
│ │ │ │ │  
│ │ │ │ │  $references$`env::69`
│ │ │ │ │ -[1] 66704  1516
│ │ │ │ │ +[1] 66716  1516
│ │ │ │ │  
│ │ │ │ │  $references$`env::7`
│ │ │ │ │ -[1] 11184   347
│ │ │ │ │ +[1] 11196   347
│ │ │ │ │  
│ │ │ │ │  $references$`env::70`
│ │ │ │ │ -[1] 205661   2473
│ │ │ │ │ +[1] 205673   2473
│ │ │ │ │  
│ │ │ │ │  $references$`env::71`
│ │ │ │ │ -[1] 191217    143
│ │ │ │ │ +[1] 191229    143
│ │ │ │ │  
│ │ │ │ │  $references$`env::72`
│ │ │ │ │ -[1] 186089   5128
│ │ │ │ │ +[1] 186101   5128
│ │ │ │ │  
│ │ │ │ │  $references$`env::73`
│ │ │ │ │ -[1] 185367    722
│ │ │ │ │ +[1] 185379    722
│ │ │ │ │  
│ │ │ │ │  $references$`env::74`
│ │ │ │ │ -[1] 76957   143
│ │ │ │ │ +[1] 76969   143
│ │ │ │ │  
│ │ │ │ │  $references$`env::75`
│ │ │ │ │ -[1] 68220  8737
│ │ │ │ │ +[1] 68232  8737
│ │ │ │ │  
│ │ │ │ │  $references$`env::76`
│ │ │ │ │ -[1] 180609   4758
│ │ │ │ │ +[1] 180621   4758
│ │ │ │ │  
│ │ │ │ │  $references$`env::77`
│ │ │ │ │ -[1] 92955 52733
│ │ │ │ │ +[1] 92967 52733
│ │ │ │ │  
│ │ │ │ │  $references$`env::78`
│ │ │ │ │ -[1] 85197   336
│ │ │ │ │ +[1] 85209   336
│ │ │ │ │  
│ │ │ │ │  $references$`env::79`
│ │ │ │ │ -[1] 78191  7006
│ │ │ │ │ +[1] 78203  7006
│ │ │ │ │  
│ │ │ │ │  $references$`env::8`
│ │ │ │ │ -[1] 11531   347
│ │ │ │ │ +[1] 11543   347
│ │ │ │ │  
│ │ │ │ │  $references$`env::80`
│ │ │ │ │ -[1] 77100  1091
│ │ │ │ │ +[1] 77112  1091
│ │ │ │ │  
│ │ │ │ │  $references$`env::81`
│ │ │ │ │ -[1] 85533  2269
│ │ │ │ │ +[1] 85545  2269
│ │ │ │ │  
│ │ │ │ │  $references$`env::82`
│ │ │ │ │ -[1] 87802  4845
│ │ │ │ │ +[1] 87814  4845
│ │ │ │ │  
│ │ │ │ │  $references$`env::83`
│ │ │ │ │ -[1] 92647   308
│ │ │ │ │ +[1] 92659   308
│ │ │ │ │  
│ │ │ │ │  $references$`env::84`
│ │ │ │ │ -[1] 145688  34921
│ │ │ │ │ +[1] 145700  34921
│ │ │ │ │  
│ │ │ │ │  $references$`env::85`
│ │ │ │ │ -[1] 197153   2511
│ │ │ │ │ +[1] 197165   2511
│ │ │ │ │  
│ │ │ │ │  $references$`env::86`
│ │ │ │ │ -[1] 196994    159
│ │ │ │ │ +[1] 197006    159
│ │ │ │ │  
│ │ │ │ │  $references$`env::87`
│ │ │ │ │ -[1] 191360   5634
│ │ │ │ │ +[1] 191372   5634
│ │ │ │ │  
│ │ │ │ │  $references$`env::88`
│ │ │ │ │ -[1] 205518    143
│ │ │ │ │ +[1] 205530    143
│ │ │ │ │  
│ │ │ │ │  $references$`env::89`
│ │ │ │ │ -[1] 200388   5130
│ │ │ │ │ +[1] 200400   5130
│ │ │ │ │  
│ │ │ │ │  $references$`env::9`
│ │ │ │ │ -[1] 17296  2253
│ │ │ │ │ +[1] 17308  2253
│ │ │ │ │  
│ │ │ │ │  $references$`env::90`
│ │ │ │ │ -[1] 199664    724
│ │ │ │ │ +[1] 199676    724
│ │ │ │ │  
│ │ │ │ │  $references$`env::91`
│ │ │ │ │ -[1] 266858  58724
│ │ │ │ │ +[1] 266870  58724
│ │ │ │ │  
│ │ │ │ │  $references$`env::92`
│ │ │ │ │ -[1] 327693    352
│ │ │ │ │ +[1] 327705    352
│ │ │ │ │  
│ │ │ │ │  $references$`env::93`
│ │ │ │ │ -[1] 327434    259
│ │ │ │ │ +[1] 327446    259
│ │ │ │ │  
│ │ │ │ │  $references$`env::94`
│ │ │ │ │ -[1] 326730    352
│ │ │ │ │ +[1] 326742    352
│ │ │ │ │  
│ │ │ │ │  $references$`env::95`
│ │ │ │ │ -[1] 327082    352
│ │ │ │ │ +[1] 327094    352
│ │ │ │ │  
│ │ │ │ │  $references$`env::96`
│ │ │ │ │ -[1] 337404   4448
│ │ │ │ │ +[1] 337416   4448
│ │ │ │ │  
│ │ │ │ │  $references$`env::97`
│ │ │ │ │ -[1] 336994    410
│ │ │ │ │ +[1] 337006    410
│ │ │ │ │  
│ │ │ │ │  $references$`env::98`
│ │ │ │ │ -[1] 328098   4448
│ │ │ │ │ +[1] 328110   4448
│ │ │ │ │  
│ │ │ │ │  $references$`env::99`
│ │ │ │ │ -[1] 332546   4448
│ │ │ │ │ +[1] 332558   4448
│ │ │ │ │  
│ │ │ │ │  
│ │ │ │ │  $compressed
│ │ │ │ │  [1] TRUE
│ │ ├── ./usr/lib/R/site-library/ballgown/doc/ballgown.html
│ │ │ @@ -103,15 +103,15 @@
│ │ │    body { max-width: 100%; }
│ │ │    tr, img { break-inside: avoid; }
│ │ │  }
│ │ │  @media only screen and (min-width: 992px) {
│ │ │    body:not(.pagesjs) pre:has(.line-numbers):not(:hover) { white-space: pre; }
│ │ │  }
│ │ │  </style>
│ │ │ -<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/@xiee/utils@1.14.69/css/prism-xcode.min.css">
│ │ │ +<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/@xiee/utils/css/prism-xcode.min.css">
│ │ │  </head>
│ │ │  <body>
│ │ │  <div class="frontmatter">
│ │ │  </div>
│ │ │  <div class="body">
│ │ │  <!--
│ │ │  %\VignetteEngine{knitr::knitr}
│ │ │ @@ -209,32 +209,32 @@
│ │ │          t_data.ctab
│ │ │  </code></pre>
│ │ │  <p>Data is loaded using the <code>ballgown</code> function.</p>
│ │ │  <p>If your data is stored in directories matching the above structure (one root folder, subfolders named by sample, and <code>.ctab</code> files in the subfolders), you can use the <code>dataDir</code> and <code>samplePattern</code> arguments to load the data. <code>samplePattern</code> takes a regular expressions specifying the subfolders that should be included in the ballgown object:</p>
│ │ │  <pre><code class="language-r">library(ballgown)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `library()`:
│ │ │ -## ! es gibt kein Paket namens 'ballgown'
│ │ │ +## ! there is no package called 'ballgown'
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">data_directory = system.file('extdata', package='ballgown') # automatically finds ballgown's installation directory
│ │ │  # examine data_directory:
│ │ │  data_directory
│ │ │  </code></pre>
│ │ │  <pre><code>## [1] &quot;&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r"># make the ballgown object:
│ │ │  bg = ballgown(dataDir=data_directory, samplePattern='sample', meas='all')
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `ballgown()`:
│ │ │ -## ! konnte Funktion &quot;ballgown&quot; nicht finden
│ │ │ +## ! could not find function &quot;ballgown&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">bg
│ │ │  </code></pre>
│ │ │  <pre><code>## Error:
│ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ +## ! object 'bg' not found
│ │ │  </code></pre>
│ │ │  <p>If your data is stored in a directory structure other than the one specified above, you can use the <code>samples</code> argument in the <code>ballgown</code> function: <code>samples</code> should be a vector (1-d array) with one entry per sample, where the entry gives the path to the folder containing that sample’s <code>.ctab</code> files.</p>
│ │ │  <p>The result from either of these approaches is an object of class <code>ballgown</code> (named <code>bg</code> in these examples).</p>
│ │ │  <p>In the rest of this document, we use <code>bg</code> to refer to the first example, where samples are named <code>sample01</code> through <code>sample20</code>.</p>
│ │ │  <p>A note for large experiments (with many samples or with large genomes): loading the data might require a lot of time and memory. In these cases, it’s often useful to do the data loading in non-interactive mode. More specifically, you could create a script called <code>load.R</code> that contains these lines:</p>
│ │ │  <pre><code class="language-R">library(ballgown)
│ │ │  data_directory = system.file('extdata', package='ballgown') 
│ │ │ @@ -250,241 +250,241 @@
│ │ │  <p>A <code>ballgown</code> object has six slots: <code>structure</code>, <code>expr</code>, <code>indexes</code>, <code>dirs</code>, <code>mergedDate</code>, and <code>meas</code>.</p>
│ │ │  <h4 id="sec:structure">structure</h4>
│ │ │  <p>The <code>structure</code> slot depends heavily on the <code>GenomicRanges</code> Bioconductor package (<a href="http://dx.doi.org/10.1371/journal.pcbi.1003118">Lawrence et al. (2013)</a>). The slot specifies the structure, i.e., genomic locations and relationships between exons, introns, and transcripts, of the transcriptome assembly.  It is convenient to represent exons and introns as intervals and to represent transcripts as a set of intervals (exons), so assembled exons and introns are available as <code>GRanges</code> objects, and the assembled transcripts are available as a <code>GRangesList</code> object.  This means that useful range operations, such as <code>findOverlaps</code> and <code>reduce</code>, are readily available for assembled features.</p>
│ │ │  <p>Exon, intron, and transcript structures are easily extracted from the main <code>ballgown</code> object:</p>
│ │ │  <pre><code class="language-r">structure(bg)$exon
│ │ │  </code></pre>
│ │ │  <pre><code>## Error:
│ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ +## ! object 'bg' not found
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">structure(bg)$intron
│ │ │  </code></pre>
│ │ │  <pre><code>## Error:
│ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ +## ! object 'bg' not found
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">structure(bg)$trans
│ │ │  </code></pre>
│ │ │  <pre><code>## Error:
│ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ +## ! object 'bg' not found
│ │ │  </code></pre>
│ │ │  <h4 id="sec:expr">expr</h4>
│ │ │  <p>The <code>expr</code> slot is a list that contains tables of expression data for the genomic features.  These tables are very similar to the <code>*_data.ctab</code> <em>Tablemaker</em> output files. Ballgown implements the following syntax to access components of the <code>expr</code> slot:</p>
│ │ │  <pre><code class="language-R">*expr(ballgown_object_name, &lt;EXPRESSION_MEASUREMENT&gt;)
│ │ │  </code></pre>
│ │ │  <p>where <code>*</code> is either e for exon, i for intron, t for transcript, or g for gene, and <EXPRESSION MEASUREMENT> is an expression-measurement column name from the appropriate <code>.ctab</code> file.  Gene-level measurements are calculated by aggregating the transcript-level measurements for that gene.  All of the following are valid ways to extract expression data from the <code>bg</code> ballgown object:</p>
│ │ │  <pre><code class="language-r">transcript_fpkm = texpr(bg, 'FPKM')
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `texpr()`:
│ │ │ -## ! konnte Funktion &quot;texpr&quot; nicht finden
│ │ │ +## ! could not find function &quot;texpr&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">transcript_cov = texpr(bg, 'cov')
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `texpr()`:
│ │ │ -## ! konnte Funktion &quot;texpr&quot; nicht finden
│ │ │ +## ! could not find function &quot;texpr&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">whole_tx_table = texpr(bg, 'all')
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `texpr()`:
│ │ │ -## ! konnte Funktion &quot;texpr&quot; nicht finden
│ │ │ +## ! could not find function &quot;texpr&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">exon_mcov = eexpr(bg, 'mcov')
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `eexpr()`:
│ │ │ -## ! konnte Funktion &quot;eexpr&quot; nicht finden
│ │ │ +## ! could not find function &quot;eexpr&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">junction_rcount = iexpr(bg)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `iexpr()`:
│ │ │ -## ! konnte Funktion &quot;iexpr&quot; nicht finden
│ │ │ +## ! could not find function &quot;iexpr&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">whole_intron_table = iexpr(bg, 'all')
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `iexpr()`:
│ │ │ -## ! konnte Funktion &quot;iexpr&quot; nicht finden
│ │ │ +## ! could not find function &quot;iexpr&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">gene_expression = gexpr(bg)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `gexpr()`:
│ │ │ -## ! konnte Funktion &quot;gexpr&quot; nicht finden
│ │ │ +## ! could not find function &quot;gexpr&quot;
│ │ │  </code></pre>
│ │ │  <p>Calculating the gene-level expression measurements can be slow for large experiments.</p>
│ │ │  <p>The <code>*expr</code> functions return matrices unless <code>meas = 'all'</code>, in which case some additional feature metadata is returned and the result is a <code>data.frame</code>.</p>
│ │ │  <h4 id="sec:indexes">indexes</h4>
│ │ │  <p>The <code>indexes</code> slot of a ballgown object connects the pieces of the assembly and provides other experimental information. <code>indexes(bg)</code> is a list with several components that can be extracted with the <code>$</code> operator.</p>
│ │ │  <p>Perhaps most importantly, there is a component called <code>pData</code> that should hold a data frame of phenotype information for the samples in the experiment. This must be created manually.  It is <strong>very important</strong> that the rows of pData are in the correct order. Each row corresponds to a sample, and the rows of pData should be ordered teh same as the tables in the <code>expr</code> slot. You can check that order by running <code>sampleNames(bg)</code>. The <code>pData</code> component can be added during construction (you can pass a data frame to the <code>ballgown</code> function), or you can add it later:</p>
│ │ │  <pre><code class="language-r">pData(bg) = data.frame(id=sampleNames(bg), group=rep(c(1,0), each=10))
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `sampleNames()`:
│ │ │ -## ! konnte Funktion &quot;sampleNames&quot; nicht finden
│ │ │ +## ! could not find function &quot;sampleNames&quot;
│ │ │  </code></pre>
│ │ │  <p>The other components of <code>indexes</code> are the <code>e2t</code> and <code>i2t</code> tables described in the <em>Tablemaker</em> section, as well as a <code>t2g</code> table denoting which transcripts belong to which genes.  There is also a <code>bamfiles</code> component, designed to hold paths to the read alignment files for each sample. The <code>bamfiles</code> component isn’t currently used by any ballgown functions, but it could come in handy for users of <code>RSamtools</code> or similar packages.  Here are some examples of how to extract <code>indexes</code> components from ballgown objects:</p>
│ │ │  <pre><code class="language-r">exon_transcript_table = indexes(bg)$e2t
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `indexes()`:
│ │ │ -## ! konnte Funktion &quot;indexes&quot; nicht finden
│ │ │ +## ! could not find function &quot;indexes&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">transcript_gene_table = indexes(bg)$t2g
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `indexes()`:
│ │ │ -## ! konnte Funktion &quot;indexes&quot; nicht finden
│ │ │ +## ! could not find function &quot;indexes&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">head(transcript_gene_table)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error:
│ │ │ -## ! Objekt 'transcript_gene_table' nicht gefunden
│ │ │ +## ! object 'transcript_gene_table' not found
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">phenotype_table = pData(bg)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `pData()`:
│ │ │ -## ! konnte Funktion &quot;pData&quot; nicht finden
│ │ │ +## ! could not find function &quot;pData&quot;
│ │ │  </code></pre>
│ │ │  <h4 id="sec:other-slots">other slots</h4>
│ │ │  <p>The <code>dirs</code> slot gives full filepaths to <em>Tablemaker</em> output:</p>
│ │ │  <pre><code class="language-r">head(bg@dirs)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error:
│ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ +## ! object 'bg' not found
│ │ │  </code></pre>
│ │ │  <p>The <code>mergedDate</code> slot indicates when the <code>ballgown</code> object was created:</p>
│ │ │  <pre><code class="language-r">bg@mergedDate
│ │ │  </code></pre>
│ │ │  <pre><code>## Error:
│ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ +## ! object 'bg' not found
│ │ │  </code></pre>
│ │ │  <p>And the <code>meas</code> slot gives the expression measurements present in the object:</p>
│ │ │  <pre><code class="language-r">bg@meas
│ │ │  </code></pre>
│ │ │  <pre><code>## Error:
│ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ +## ! object 'bg' not found
│ │ │  </code></pre>
│ │ │  <h1 id="chp:plotting-transcript-structures">Plotting transcript structures</h1>
│ │ │  <p>Visualization of the assembled transcripts is done with the <code>plotTranscripts</code> function. Transcripts or exons can be colored by expression level. This plot colors transcripts by expression level:</p>
│ │ │  <pre><code class="language-r">plotTranscripts(gene='XLOC_000454', gown=bg, samples='sample12', 
│ │ │      meas='FPKM', colorby='transcript', 
│ │ │      main='transcripts from gene XLOC_000454: sample 12, FPKM')
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `plotTranscripts()`:
│ │ │ -## ! konnte Funktion &quot;plotTranscripts&quot; nicht finden
│ │ │ +## ! could not find function &quot;plotTranscripts&quot;
│ │ │  </code></pre>
│ │ │  <p>It is also possible to plot several samples at once:</p>
│ │ │  <pre><code class="language-r">plotTranscripts('XLOC_000454', bg, 
│ │ │      samples=c('sample01', 'sample06', 'sample12', 'sample19'), 
│ │ │      meas='FPKM', colorby='transcript')
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `plotTranscripts()`:
│ │ │ -## ! konnte Funktion &quot;plotTranscripts&quot; nicht finden
│ │ │ +## ! could not find function &quot;plotTranscripts&quot;
│ │ │  </code></pre>
│ │ │  <p>You can also make side-by-side plots comparing mean abundances between groups (here, 0 and 1):</p>
│ │ │  <pre><code class="language-r">plotMeans('XLOC_000454', bg, groupvar='group', meas='FPKM', colorby='transcript')
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `plotMeans()`:
│ │ │ -## ! konnte Funktion &quot;plotMeans&quot; nicht finden
│ │ │ +## ! could not find function &quot;plotMeans&quot;
│ │ │  </code></pre>
│ │ │  <h1 id="chp:differential-expression-analysis">Differential expression analysis</h1>
│ │ │  <p>Ballgown provides a wide selection of simple, fast statistical methods for testing whether transcripts are differentially expressed between experimental conditions or across a continuous covariate (such as time).</p>
│ │ │  <p>The default statistical test in ballgown is a parametric F-test comparing nested linear models; details are available in the Ballgown manuscript (<a href="http://biorxiv.org/content/early/2014/03/30/003665">Frazee et al. (2014)</a>). These models are conceptually simialar to the models used by <a href="http://link.springer.com/chapter/10.1007%2F0-387-29362-0_23">Smyth (2005)</a> in the <code>limma</code> package. In <code>limma</code>, more sophisticated empirical Bayes shrinkage methods are used, and generally a single linear model is fit per feature instead of doing a nested model comparison, but the flavor is similar (and in fact, <code>limma</code> can easily be run on any of the data matrices in a <code>ballgown</code> object).</p>
│ │ │  <p>Ballgown’s statistical models are implemented with the <code>stattest</code> function. Two models are fit to each feature, using expression as the outcome: one including the covariate of interest (e.g., case/control status or time) and one not including that covariate. An F statistic and p-value are calculated using the fits of the two models. A significant p-value means the model including the covariate of interest fits significantly better than the model without that covariate, indicating differential expression. We adjust for multiple testing by reporting q-values (<a href="http://dx.doi.org/10.1073/pnas.1530509100">Storey &amp; Tibshirani (2003)</a>) for each transcript in addition to p-values: reporting features with, say, q &lt; 0.05 means the false discovery rate should be controlled at about 5%.</p>
│ │ │  <p><code>stattest</code> automatically handles two-group (e.g. case/control) comparisons, multi-group comparisons (e.g. comparison of several tissue types), and “timecourse” comparisons (with the scare quotes meaning that these comparisons are also applicable to continuous covariates that aren’t time). For two- and multi-group comparisons, a significant result indicates that the feature is differentially expressed in at least one of the groups. For timecourse comparisions, significant results mean the feature has an expression profile that varies significantly over time (i.e., values of the continuous covariate) as opposed to being flat over time.</p>
│ │ │  <p>The example dataset <code>bg</code> contains two group labels, 0 and 1. We can test each transcript for differential expression with <code>stattest</code>:</p>
│ │ │  <pre><code class="language-r">stat_results = stattest(bg, feature='transcript', meas='FPKM', covariate='group')
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `stattest()`:
│ │ │ -## ! konnte Funktion &quot;stattest&quot; nicht finden
│ │ │ +## ! could not find function &quot;stattest&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">head(stat_results)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error:
│ │ │ -## ! Objekt 'stat_results' nicht gefunden
│ │ │ +## ! object 'stat_results' not found
│ │ │  </code></pre>
│ │ │  <p>The result is a data frame containing the feature tested, feature ids, and corresponding p- and q-values. See <code>?stattest</code> for further usage details.</p>
│ │ │  <h4 id="sec:timecourse-experiments">timecourse experiments</h4>
│ │ │  <p>For timecourse experiments, a smooth curve is fit to time (or the continuous covariate) using <a href="http://en.wikipedia.org/wiki/Spline_interpolation">natural splines</a>. The default degrees of freedom used for the spline model is 4, but this can be adjusted with the <code>df</code> option. The model for expression including these spline terms is compared to a model without any spline terms for the F-test. The results indicate which features’ expression levels change significantly over time. For our example, we can define a “time” covariate and then demonstrate a typical call to <code>stattest</code> for a timecourse experiment:</p>
│ │ │  <pre><code class="language-r">pData(bg) = data.frame(pData(bg), time=rep(1:10, 2)) #dummy time covariate
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `pData()`:
│ │ │ -## ! konnte Funktion &quot;pData&quot; nicht finden
│ │ │ +## ! could not find function &quot;pData&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">timecourse_results = stattest(bg, feature='transcript', meas='FPKM', covariate='time', timecourse=TRUE)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `stattest()`:
│ │ │ -## ! konnte Funktion &quot;stattest&quot; nicht finden
│ │ │ +## ! could not find function &quot;stattest&quot;
│ │ │  </code></pre>
│ │ │  <p>The timecourse option assumes that “time” in your study is truly continuous, i.e., that it takes several values along a time scale. If you have very few timepoints (e.g., fewer than 5), we recommend treating time as a categorical variable, since having very few values does not give much granularity for fitting a smooth curve using splines. You can do this by setting covariate equal to ‘time’ (or whatever your time variable is named) and simply leaving timecourse as FALSE, its default. If you don’t have more timepoints than degrees of freedom in the spline model, a warning will be printed and time will be coerced to categorical.</p>
│ │ │  <h4 id="sec:adjusting-for-confounders">adjusting for confounders</h4>
│ │ │  <p>You can adjust for any or all variables in <code>pData</code> when testing for differential expression.  Ballgown automatically adjusts for library size using the sum of all logged nonzero expression measurements below the 75th percentile of those measurements, for each sample.  If you would like to adjust for other variables, just provide those confounders as the <code>adjustvars</code> argument to <code>stattest</code>:</p>
│ │ │  <pre><code class="language-r">group_adj_timecourse_results = stattest(bg, feature='transcript', meas='FPKM', covariate='time', 
│ │ │      timecourse=TRUE, adjustvars='group')
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `stattest()`:
│ │ │ -## ! konnte Funktion &quot;stattest&quot; nicht finden
│ │ │ +## ! could not find function &quot;stattest&quot;
│ │ │  </code></pre>
│ │ │  <h4 id="sec:defining-custom-models">defining custom models</h4>
│ │ │  <p>It is also possible to explicitly provide the design matrices for the models to be compared. You can provide any two models for <code>mod</code> and <code>mod0</code>, provided that <code>mod0</code> is nested in <code>mod</code>, i.e., that all covariates used in <code>mod0</code> also appear in <code>mod</code>. For example, suppose we had sex and age information available, in addition to group and time, and we wanted to compare a model (<code>mod</code>) including all information (sex, age, group, time) to a model including only group and time (<code>mod</code>). Code to do this with <code>ballgown</code> is:</p>
│ │ │  <pre><code class="language-r"># create example data:
│ │ │  set.seed(43)
│ │ │  sex = sample(c('M','F'), size=nrow(pData(bg)), replace=TRUE)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `pData()`:
│ │ │ -## ! konnte Funktion &quot;pData&quot; nicht finden
│ │ │ +## ! could not find function &quot;pData&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">age = sample(21:52, size=nrow(pData(bg)), replace=TRUE)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `pData()`:
│ │ │ -## ! konnte Funktion &quot;pData&quot; nicht finden
│ │ │ +## ! could not find function &quot;pData&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r"># create design matrices:
│ │ │  mod = model.matrix(~ sex + age + pData(bg)$group + pData(bg)$time)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error:
│ │ │ -## ! Objekt 'sex' nicht gefunden
│ │ │ +## ! object 'sex' not found
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">mod0 = model.matrix(~ pData(bg)$group + pData(bg)$time)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `pData()`:
│ │ │ -## ! konnte Funktion &quot;pData&quot; nicht finden
│ │ │ +## ! could not find function &quot;pData&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r"># run differential expression tests:
│ │ │  adjusted_results = stattest(bg, feature='transcript', meas='FPKM', mod0=mod0, mod=mod)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `stattest()`:
│ │ │ -## ! konnte Funktion &quot;stattest&quot; nicht finden
│ │ │ +## ! could not find function &quot;stattest&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">head(adjusted_results)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error:
│ │ │ -## ! Objekt 'adjusted_results' nicht gefunden
│ │ │ +## ! object 'adjusted_results' not found
│ │ │  </code></pre>
│ │ │  <h1 id="chp:using-alternative-statistical-methods">Using alternative statistical methods</h1>
│ │ │  <p>Ballgown’s statistical methods for differential expression testing are straightforward and accurate (<a href="http://biorxiv.org/content/early/2014/03/30/003665">Frazee et al. (2014)</a>), but users may wish to use one of the many existing packages for differential expression. Ballgown’s data structures make it easy to use table-based packages like limma (<a href="">Smyth (2005)</a>), limma Voom (<a href="http://dx.doi.org/10.1186/gb-2014-15-2-r29">Law et al. (2014)</a>), DESeq (<a href="http://dx.doi.org/10.1186/gb-2010-11-10-r106">Anders &amp; Huber (2010)</a>), DEXSeq (<a href="http://dx.doi.org/10.1101/gr.133744.111">Anders et al. (2012)</a>), or EdgeR (<a href="http://dx.doi.org/10.1093/bioinformatics/btp616">Robinson et al. (2010)</a>) for differential expression analysis.  A feature-by-sample expression table can be easily created with a <code>*expr</code> function and used directly as input to these or other differential expression packages.</p>
│ │ │  <h1 id="chp:simple-transcript-clustering">Simple transcript clustering</h1>
│ │ │  <p>Sometimes several very similar transcripts are assembled for the same gene, which might cause expression estimates for those transcripts to be unreliable: statistically, it can very difficult or impossible to tell which of two very similar transcript a read came from. This means differential expression results might also be unreliable.</p>
│ │ │  <p>As a preliminary attempt at addressing this issue, Ballgown provides some simple transcript clustering functions. The idea is that similar assembled transcripts can be grouped together in clusters, and differential expression analysis could be performed on the cluster, whose expression measurement aggregates the expression estimates of the transcripts that compose it.</p>
│ │ │  <p>These functions measure the distance between transcripts using <a href="http://en.wikipedia.org/wiki/Jaccard_index">Jaccard distance</a>, where each transcript’s “set” is the nucleotides included in its exons. Transcripts can be clustered using either <em>k</em>-means clustering or hierarchical clustering.</p>
│ │ │  <pre><code class="language-r">clusterTranscripts(gene='XLOC_000454', gown=bg, k=2, method='kmeans')
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `clusterTranscripts()`:
│ │ │ -## ! konnte Funktion &quot;clusterTranscripts&quot; nicht finden
│ │ │ +## ! could not find function &quot;clusterTranscripts&quot;
│ │ │  </code></pre>
│ │ │  <p>You can also visualize the transcript clusters:</p>
│ │ │  <pre><code class="language-r">plotLatentTranscripts(gene='XLOC_000454', gown=bg, k=2, method='kmeans', returncluster=FALSE)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `plotLatentTranscripts()`:
│ │ │ -## ! konnte Funktion &quot;plotLatentTranscripts&quot; nicht finden
│ │ │ +## ! could not find function &quot;plotLatentTranscripts&quot;
│ │ │  </code></pre>
│ │ │  <p>And you can calculate aggregate cluster expression measurements for some gene using <code>collapseTranscripts</code>. The <code>tab</code> result of <code>collapseTranscripts</code> can be passed to <code>stattest</code> as the <code>gowntable</code> argument, for differential expression analysis of the clusters:</p>
│ │ │  <pre><code class="language-r">agg = collapseTranscripts(gene='XLOC_000454', gown=bg, k=2, method='kmeans')
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `collapseTranscripts()`:
│ │ │ -## ! konnte Funktion &quot;collapseTranscripts&quot; nicht finden
│ │ │ +## ! could not find function &quot;collapseTranscripts&quot;
│ │ │  </code></pre>
│ │ │  <pre><code class="language-r">stattest(gowntable=agg$tab, pData=pData(bg), feature='transcript_cluster', 
│ │ │      covariate='group', libadjust=FALSE)
│ │ │  </code></pre>
│ │ │  <pre><code>## Error in `stattest()`:
│ │ │ -## ! konnte Funktion &quot;stattest&quot; nicht finden
│ │ │ +## ! could not find function &quot;stattest&quot;
│ │ │  </code></pre>
│ │ │  <p>This example clustered only three transcripts, but we imagine clustering could be useful when many more than three transcripts have been assembled for a single gene.</p>
│ │ │  <h1 id="chp:references">References</h1>
│ │ │  <ul>
│ │ │  <li>Simon Anders, Wolfgang Huber (2010). Differential Expression Analysis For Sequence Count Data.  <em>Genome Biology</em>  <strong>11</strong>  R106-NA  <a href="http://dx.doi.org/10.1186/gb-2010-11-10-r106">10.1186/gb-2010-11-10-r106</a></li>
│ │ │  <li>Simon Anders, Alejandro Reyes, Wolfgang Huber (2012). Detecting Differential Usage of Exons From RNA-Seq Data.  <em>Genome Research</em>  <strong>22</strong>  2008-2017  <a href="http://dx.doi.org/10.1101/gr.133744.111">10.1101/gr.133744.111</a></li>
│ │ │  <li>Alyssa C. Frazee, Geo Pertea, Andrew E. Jaffe, Ben Langmead, Steven L. Salzberg, Jeffrey T. Leek (2014). Flexible isoform-level differential expression analysis with Ballgown.  <em>bioRxiv</em>  <a href="http://biorxiv.org/content/early/2014/03/30/003665">http://biorxiv.org/content/early/2014/03/30/003665</a></li>
│ │ │ @@ -505,33 +505,30 @@
│ │ │  ## Running under: Debian GNU/Linux forky/sid
│ │ │  ## 
│ │ │  ## Matrix products: default
│ │ │  ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
│ │ │  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.33.so;  LAPACK version 3.12.0
│ │ │  ## 
│ │ │  ## locale:
│ │ │ -##  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
│ │ │ -##  [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
│ │ │ -##  [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
│ │ │ -##  [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
│ │ │ -##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
│ │ │ -## [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
│ │ │ +##  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
│ │ │ +##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
│ │ │ +##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
│ │ │ +## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
│ │ │  ## 
│ │ │ -## time zone: Europe/Berlin
│ │ │ +## time zone: Etc/UTC
│ │ │  ## tzcode source: system (glibc)
│ │ │  ## 
│ │ │  ## attached base packages:
│ │ │  ## [1] stats     graphics  grDevices utils     datasets  methods   base     
│ │ │  ## 
│ │ │  ## other attached packages:
│ │ │  ## [1] markdown_2.0 knitr_1.51  
│ │ │  ## 
│ │ │  ## loaded via a namespace (and not attached):
│ │ │ -##  [1] compiler_4.6.1  cli_3.6.6       tools_4.6.1     pillar_1.11.1  
│ │ │ -##  [5] otel_0.2.0      glue_1.8.1      vctrs_0.7.3     xfun_0.60      
│ │ │ -##  [9] lifecycle_1.0.5 rlang_1.3.0     evaluate_1.0.5
│ │ │ +## [1] compiler_4.6.1 cli_3.6.6      tools_4.6.1    xfun_0.60      rlang_1.3.0   
│ │ │ +## [6] evaluate_1.0.5
│ │ │  </code></pre>
│ │ │  </div>
│ │ │  <script src="https://cdn.jsdelivr.net/npm/prismjs@1.29.0/components/prism-core.min.js" defer></script>
│ │ │  <script src="https://cdn.jsdelivr.net/npm/prismjs@1.29.0/plugins/autoloader/prism-autoloader.min.js" defer></script>
│ │ │  </body>
│ │ │  </html>
│ │ │ ├── html2text {}
│ │ │ │ @@ -114,27 +114,27 @@
│ │ │ │  If your data is stored in directories matching the above structure (one root
│ │ │ │  folder, subfolders named by sample, and .ctab files in the subfolders), you can
│ │ │ │  use the dataDir and samplePattern arguments to load the data. samplePattern
│ │ │ │  takes a regular expressions specifying the subfolders that should be included
│ │ │ │  in the ballgown object:
│ │ │ │  library(ballgown)
│ │ │ │  ## Error in `library()`:
│ │ │ │ -## ! es gibt kein Paket namens 'ballgown'
│ │ │ │ +## ! there is no package called 'ballgown'
│ │ │ │  data_directory = system.file('extdata', package='ballgown') # automatically
│ │ │ │  finds ballgown's installation directory
│ │ │ │  # examine data_directory:
│ │ │ │  data_directory
│ │ │ │  ## [1] ""
│ │ │ │  # make the ballgown object:
│ │ │ │  bg = ballgown(dataDir=data_directory, samplePattern='sample', meas='all')
│ │ │ │  ## Error in `ballgown()`:
│ │ │ │ -## ! konnte Funktion "ballgown" nicht finden
│ │ │ │ +## ! could not find function "ballgown"
│ │ │ │  bg
│ │ │ │  ## Error:
│ │ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ │ +## ! object 'bg' not found
│ │ │ │  If your data is stored in a directory structure other than the one specified
│ │ │ │  above, you can use the samples argument in the ballgown function: samples
│ │ │ │  should be a vector (1-d array) with one entry per sample, where the entry gives
│ │ │ │  the path to the folder containing that sample’s .ctab files.
│ │ │ │  The result from either of these approaches is an object of class ballgown
│ │ │ │  (named bg in these examples).
│ │ │ │  In the rest of this document, we use bg to refer to the first example, where
│ │ │ │ @@ -171,53 +171,53 @@
│ │ │ │  transcripts are available as a GRangesList object. This means that useful range
│ │ │ │  operations, such as findOverlaps and reduce, are readily available for
│ │ │ │  assembled features.
│ │ │ │  Exon, intron, and transcript structures are easily extracted from the main
│ │ │ │  ballgown object:
│ │ │ │  structure(bg)$exon
│ │ │ │  ## Error:
│ │ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ │ +## ! object 'bg' not found
│ │ │ │  structure(bg)$intron
│ │ │ │  ## Error:
│ │ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ │ +## ! object 'bg' not found
│ │ │ │  structure(bg)$trans
│ │ │ │  ## Error:
│ │ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ │ +## ! object 'bg' not found
│ │ │ │  ****** eexxpprr ******
│ │ │ │  The expr slot is a list that contains tables of expression data for the genomic
│ │ │ │  features. These tables are very similar to the *_data.ctab TTaabblleemmaakkeerr output
│ │ │ │  files. Ballgown implements the following syntax to access components of the
│ │ │ │  expr slot:
│ │ │ │  *expr(ballgown_object_name, <EXPRESSION_MEASUREMENT>)
│ │ │ │  where * is either e for exon, i for intron, t for transcript, or g for gene,
│ │ │ │  and is an expression-measurement column name from the appropriate .ctab file.
│ │ │ │  Gene-level measurements are calculated by aggregating the transcript-level
│ │ │ │  measurements for that gene. All of the following are valid ways to extract
│ │ │ │  expression data from the bg ballgown object:
│ │ │ │  transcript_fpkm = texpr(bg, 'FPKM')
│ │ │ │  ## Error in `texpr()`:
│ │ │ │ -## ! konnte Funktion "texpr" nicht finden
│ │ │ │ +## ! could not find function "texpr"
│ │ │ │  transcript_cov = texpr(bg, 'cov')
│ │ │ │  ## Error in `texpr()`:
│ │ │ │ -## ! konnte Funktion "texpr" nicht finden
│ │ │ │ +## ! could not find function "texpr"
│ │ │ │  whole_tx_table = texpr(bg, 'all')
│ │ │ │  ## Error in `texpr()`:
│ │ │ │ -## ! konnte Funktion "texpr" nicht finden
│ │ │ │ +## ! could not find function "texpr"
│ │ │ │  exon_mcov = eexpr(bg, 'mcov')
│ │ │ │  ## Error in `eexpr()`:
│ │ │ │ -## ! konnte Funktion "eexpr" nicht finden
│ │ │ │ +## ! could not find function "eexpr"
│ │ │ │  junction_rcount = iexpr(bg)
│ │ │ │  ## Error in `iexpr()`:
│ │ │ │ -## ! konnte Funktion "iexpr" nicht finden
│ │ │ │ +## ! could not find function "iexpr"
│ │ │ │  whole_intron_table = iexpr(bg, 'all')
│ │ │ │  ## Error in `iexpr()`:
│ │ │ │ -## ! konnte Funktion "iexpr" nicht finden
│ │ │ │ +## ! could not find function "iexpr"
│ │ │ │  gene_expression = gexpr(bg)
│ │ │ │  ## Error in `gexpr()`:
│ │ │ │ -## ! konnte Funktion "gexpr" nicht finden
│ │ │ │ +## ! could not find function "gexpr"
│ │ │ │  Calculating the gene-level expression measurements can be slow for large
│ │ │ │  experiments.
│ │ │ │  The *expr functions return matrices unless meas = 'all', in which case some
│ │ │ │  additional feature metadata is returned and the result is a data.frame.
│ │ │ │  ****** iinnddeexxeess ******
│ │ │ │  The indexes slot of a ballgown object connects the pieces of the assembly and
│ │ │ │  provides other experimental information. indexes(bg) is a list with several
│ │ │ │ @@ -228,68 +228,68 @@
│ │ │ │  the correct order. Each row corresponds to a sample, and the rows of pData
│ │ │ │  should be ordered teh same as the tables in the expr slot. You can check that
│ │ │ │  order by running sampleNames(bg). The pData component can be added during
│ │ │ │  construction (you can pass a data frame to the ballgown function), or you can
│ │ │ │  add it later:
│ │ │ │  pData(bg) = data.frame(id=sampleNames(bg), group=rep(c(1,0), each=10))
│ │ │ │  ## Error in `sampleNames()`:
│ │ │ │ -## ! konnte Funktion "sampleNames" nicht finden
│ │ │ │ +## ! could not find function "sampleNames"
│ │ │ │  The other components of indexes are the e2t and i2t tables described in the
│ │ │ │  TTaabblleemmaakkeerr section, as well as a t2g table denoting which transcripts belong to
│ │ │ │  which genes. There is also a bamfiles component, designed to hold paths to the
│ │ │ │  read alignment files for each sample. The bamfiles component isn’t currently
│ │ │ │  used by any ballgown functions, but it could come in handy for users of
│ │ │ │  RSamtools or similar packages. Here are some examples of how to extract indexes
│ │ │ │  components from ballgown objects:
│ │ │ │  exon_transcript_table = indexes(bg)$e2t
│ │ │ │  ## Error in `indexes()`:
│ │ │ │ -## ! konnte Funktion "indexes" nicht finden
│ │ │ │ +## ! could not find function "indexes"
│ │ │ │  transcript_gene_table = indexes(bg)$t2g
│ │ │ │  ## Error in `indexes()`:
│ │ │ │ -## ! konnte Funktion "indexes" nicht finden
│ │ │ │ +## ! could not find function "indexes"
│ │ │ │  head(transcript_gene_table)
│ │ │ │  ## Error:
│ │ │ │ -## ! Objekt 'transcript_gene_table' nicht gefunden
│ │ │ │ +## ! object 'transcript_gene_table' not found
│ │ │ │  phenotype_table = pData(bg)
│ │ │ │  ## Error in `pData()`:
│ │ │ │ -## ! konnte Funktion "pData" nicht finden
│ │ │ │ +## ! could not find function "pData"
│ │ │ │  ****** ootthheerr sslloottss ******
│ │ │ │  The dirs slot gives full filepaths to TTaabblleemmaakkeerr output:
│ │ │ │  head(bg@dirs)
│ │ │ │  ## Error:
│ │ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ │ +## ! object 'bg' not found
│ │ │ │  The mergedDate slot indicates when the ballgown object was created:
│ │ │ │  bg@mergedDate
│ │ │ │  ## Error:
│ │ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ │ +## ! object 'bg' not found
│ │ │ │  And the meas slot gives the expression measurements present in the object:
│ │ │ │  bg@meas
│ │ │ │  ## Error:
│ │ │ │ -## ! Objekt 'bg' nicht gefunden
│ │ │ │ +## ! object 'bg' not found
│ │ │ │  ************ PPlloottttiinngg ttrraannssccrriipptt ssttrruuccttuurreess ************
│ │ │ │  Visualization of the assembled transcripts is done with the plotTranscripts
│ │ │ │  function. Transcripts or exons can be colored by expression level. This plot
│ │ │ │  colors transcripts by expression level:
│ │ │ │  plotTranscripts(gene='XLOC_000454', gown=bg, samples='sample12',
│ │ │ │      meas='FPKM', colorby='transcript',
│ │ │ │      main='transcripts from gene XLOC_000454: sample 12, FPKM')
│ │ │ │  ## Error in `plotTranscripts()`:
│ │ │ │ -## ! konnte Funktion "plotTranscripts" nicht finden
│ │ │ │ +## ! could not find function "plotTranscripts"
│ │ │ │  It is also possible to plot several samples at once:
│ │ │ │  plotTranscripts('XLOC_000454', bg,
│ │ │ │      samples=c('sample01', 'sample06', 'sample12', 'sample19'),
│ │ │ │      meas='FPKM', colorby='transcript')
│ │ │ │  ## Error in `plotTranscripts()`:
│ │ │ │ -## ! konnte Funktion "plotTranscripts" nicht finden
│ │ │ │ +## ! could not find function "plotTranscripts"
│ │ │ │  You can also make side-by-side plots comparing mean abundances between groups
│ │ │ │  (here, 0 and 1):
│ │ │ │  plotMeans('XLOC_000454', bg, groupvar='group', meas='FPKM',
│ │ │ │  colorby='transcript')
│ │ │ │  ## Error in `plotMeans()`:
│ │ │ │ -## ! konnte Funktion "plotMeans" nicht finden
│ │ │ │ +## ! could not find function "plotMeans"
│ │ │ │  ************ DDiiffffeerreennttiiaall eexxpprreessssiioonn aannaallyyssiiss ************
│ │ │ │  Ballgown provides a wide selection of simple, fast statistical methods for
│ │ │ │  testing whether transcripts are differentially expressed between experimental
│ │ │ │  conditions or across a continuous covariate (such as time).
│ │ │ │  The default statistical test in ballgown is a parametric F-test comparing
│ │ │ │  nested linear models; details are available in the Ballgown manuscript (_F_r_a_z_e_e
│ │ │ │  _e_t_ _a_l_._ _(_2_0_1_4_)). These models are conceptually simialar to the models used by
│ │ │ │ @@ -318,36 +318,36 @@
│ │ │ │  that varies significantly over time (i.e., values of the continuous covariate)
│ │ │ │  as opposed to being flat over time.
│ │ │ │  The example dataset bg contains two group labels, 0 and 1. We can test each
│ │ │ │  transcript for differential expression with stattest:
│ │ │ │  stat_results = stattest(bg, feature='transcript', meas='FPKM',
│ │ │ │  covariate='group')
│ │ │ │  ## Error in `stattest()`:
│ │ │ │ -## ! konnte Funktion "stattest" nicht finden
│ │ │ │ +## ! could not find function "stattest"
│ │ │ │  head(stat_results)
│ │ │ │  ## Error:
│ │ │ │ -## ! Objekt 'stat_results' nicht gefunden
│ │ │ │ +## ! object 'stat_results' not found
│ │ │ │  The result is a data frame containing the feature tested, feature ids, and
│ │ │ │  corresponding p- and q-values. See ?stattest for further usage details.
│ │ │ │  ****** ttiimmeeccoouurrssee eexxppeerriimmeennttss ******
│ │ │ │  For timecourse experiments, a smooth curve is fit to time (or the continuous
│ │ │ │  covariate) using _n_a_t_u_r_a_l_ _s_p_l_i_n_e_s. The default degrees of freedom used for the
│ │ │ │  spline model is 4, but this can be adjusted with the df option. The model for
│ │ │ │  expression including these spline terms is compared to a model without any
│ │ │ │  spline terms for the F-test. The results indicate which features’ expression
│ │ │ │  levels change significantly over time. For our example, we can define a “time”
│ │ │ │  covariate and then demonstrate a typical call to stattest for a timecourse
│ │ │ │  experiment:
│ │ │ │  pData(bg) = data.frame(pData(bg), time=rep(1:10, 2)) #dummy time covariate
│ │ │ │  ## Error in `pData()`:
│ │ │ │ -## ! konnte Funktion "pData" nicht finden
│ │ │ │ +## ! could not find function "pData"
│ │ │ │  timecourse_results = stattest(bg, feature='transcript', meas='FPKM',
│ │ │ │  covariate='time', timecourse=TRUE)
│ │ │ │  ## Error in `stattest()`:
│ │ │ │ -## ! konnte Funktion "stattest" nicht finden
│ │ │ │ +## ! could not find function "stattest"
│ │ │ │  The timecourse option assumes that “time” in your study is truly continuous,
│ │ │ │  i.e., that it takes several values along a time scale. If you have very few
│ │ │ │  timepoints (e.g., fewer than 5), we recommend treating time as a categorical
│ │ │ │  variable, since having very few values does not give much granularity for
│ │ │ │  fitting a smooth curve using splines. You can do this by setting covariate
│ │ │ │  equal to ‘time’ (or whatever your time variable is named) and simply leaving
│ │ │ │  timecourse as FALSE, its default. If you don’t have more timepoints than
│ │ │ │ @@ -359,46 +359,46 @@
│ │ │ │  all logged nonzero expression measurements below the 75th percentile of those
│ │ │ │  measurements, for each sample. If you would like to adjust for other variables,
│ │ │ │  just provide those confounders as the adjustvars argument to stattest:
│ │ │ │  group_adj_timecourse_results = stattest(bg, feature='transcript', meas='FPKM',
│ │ │ │  covariate='time',
│ │ │ │      timecourse=TRUE, adjustvars='group')
│ │ │ │  ## Error in `stattest()`:
│ │ │ │ -## ! konnte Funktion "stattest" nicht finden
│ │ │ │ +## ! could not find function "stattest"
│ │ │ │  ****** ddeeffiinniinngg ccuussttoomm mmooddeellss ******
│ │ │ │  It is also possible to explicitly provide the design matrices for the models to
│ │ │ │  be compared. You can provide any two models for mod and mod0, provided that
│ │ │ │  mod0 is nested in mod, i.e., that all covariates used in mod0 also appear in
│ │ │ │  mod. For example, suppose we had sex and age information available, in addition
│ │ │ │  to group and time, and we wanted to compare a model (mod) including all
│ │ │ │  information (sex, age, group, time) to a model including only group and time
│ │ │ │  (mod). Code to do this with ballgown is:
│ │ │ │  # create example data:
│ │ │ │  set.seed(43)
│ │ │ │  sex = sample(c('M','F'), size=nrow(pData(bg)), replace=TRUE)
│ │ │ │  ## Error in `pData()`:
│ │ │ │ -## ! konnte Funktion "pData" nicht finden
│ │ │ │ +## ! could not find function "pData"
│ │ │ │  age = sample(21:52, size=nrow(pData(bg)), replace=TRUE)
│ │ │ │  ## Error in `pData()`:
│ │ │ │ -## ! konnte Funktion "pData" nicht finden
│ │ │ │ +## ! could not find function "pData"
│ │ │ │  # create design matrices:
│ │ │ │  mod = model.matrix(~ sex + age + pData(bg)$group + pData(bg)$time)
│ │ │ │  ## Error:
│ │ │ │ -## ! Objekt 'sex' nicht gefunden
│ │ │ │ +## ! object 'sex' not found
│ │ │ │  mod0 = model.matrix(~ pData(bg)$group + pData(bg)$time)
│ │ │ │  ## Error in `pData()`:
│ │ │ │ -## ! konnte Funktion "pData" nicht finden
│ │ │ │ +## ! could not find function "pData"
│ │ │ │  # run differential expression tests:
│ │ │ │  adjusted_results = stattest(bg, feature='transcript', meas='FPKM', mod0=mod0,
│ │ │ │  mod=mod)
│ │ │ │  ## Error in `stattest()`:
│ │ │ │ -## ! konnte Funktion "stattest" nicht finden
│ │ │ │ +## ! could not find function "stattest"
│ │ │ │  head(adjusted_results)
│ │ │ │  ## Error:
│ │ │ │ -## ! Objekt 'adjusted_results' nicht gefunden
│ │ │ │ +## ! object 'adjusted_results' not found
│ │ │ │  ************ UUssiinngg aalltteerrnnaattiivvee ssttaattiissttiiccaall mmeetthhooddss ************
│ │ │ │  Ballgown’s statistical methods for differential expression testing are
│ │ │ │  straightforward and accurate (_F_r_a_z_e_e_ _e_t_ _a_l_._ _(_2_0_1_4_)), but users may wish to use
│ │ │ │  one of the many existing packages for differential expression. Ballgown’s data
│ │ │ │  structures make it easy to use table-based packages like limma (Smyth (2005)),
│ │ │ │  limma Voom (_L_a_w_ _e_t_ _a_l_._ _(_2_0_1_4_)), DESeq (_A_n_d_e_r_s_ _&_ _H_u_b_e_r_ _(_2_0_1_0_)), DEXSeq (_A_n_d_e_r_s
│ │ │ │  _e_t_ _a_l_._ _(_2_0_1_2_)), or EdgeR (_R_o_b_i_n_s_o_n_ _e_t_ _a_l_._ _(_2_0_1_0_)) for differential expression
│ │ │ │ @@ -418,31 +418,31 @@
│ │ │ │  aggregates the expression estimates of the transcripts that compose it.
│ │ │ │  These functions measure the distance between transcripts using _J_a_c_c_a_r_d
│ │ │ │  _d_i_s_t_a_n_c_e, where each transcript’s “set” is the nucleotides included in its
│ │ │ │  exons. Transcripts can be clustered using either kk-means clustering or
│ │ │ │  hierarchical clustering.
│ │ │ │  clusterTranscripts(gene='XLOC_000454', gown=bg, k=2, method='kmeans')
│ │ │ │  ## Error in `clusterTranscripts()`:
│ │ │ │ -## ! konnte Funktion "clusterTranscripts" nicht finden
│ │ │ │ +## ! could not find function "clusterTranscripts"
│ │ │ │  You can also visualize the transcript clusters:
│ │ │ │  plotLatentTranscripts(gene='XLOC_000454', gown=bg, k=2, method='kmeans',
│ │ │ │  returncluster=FALSE)
│ │ │ │  ## Error in `plotLatentTranscripts()`:
│ │ │ │ -## ! konnte Funktion "plotLatentTranscripts" nicht finden
│ │ │ │ +## ! could not find function "plotLatentTranscripts"
│ │ │ │  And you can calculate aggregate cluster expression measurements for some gene
│ │ │ │  using collapseTranscripts. The tab result of collapseTranscripts can be passed
│ │ │ │  to stattest as the gowntable argument, for differential expression analysis of
│ │ │ │  the clusters:
│ │ │ │  agg = collapseTranscripts(gene='XLOC_000454', gown=bg, k=2, method='kmeans')
│ │ │ │  ## Error in `collapseTranscripts()`:
│ │ │ │ -## ! konnte Funktion "collapseTranscripts" nicht finden
│ │ │ │ +## ! could not find function "collapseTranscripts"
│ │ │ │  stattest(gowntable=agg$tab, pData=pData(bg), feature='transcript_cluster',
│ │ │ │      covariate='group', libadjust=FALSE)
│ │ │ │  ## Error in `stattest()`:
│ │ │ │ -## ! konnte Funktion "stattest" nicht finden
│ │ │ │ +## ! could not find function "stattest"
│ │ │ │  This example clustered only three transcripts, but we imagine clustering could
│ │ │ │  be useful when many more than three transcripts have been assembled for a
│ │ │ │  single gene.
│ │ │ │  ************ RReeffeerreenncceess ************
│ │ │ │      * Simon Anders, Wolfgang Huber (2010). Differential Expression Analysis For
│ │ │ │        Sequence Count Data. GGeennoommee BBiioollooggyy 1111 R106-NA _1_0_._1_1_8_6_/_g_b_-_2_0_1_0_-_1_1_-_1_0_-_r_1_0_6
│ │ │ │      * Simon Anders, Alejandro Reyes, Wolfgang Huber (2012). Detecting
│ │ │ │ @@ -480,27 +480,25 @@
│ │ │ │  ##
│ │ │ │  ## Matrix products: default
│ │ │ │  ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
│ │ │ │  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.33.so;
│ │ │ │  LAPACK version 3.12.0
│ │ │ │  ##
│ │ │ │  ## locale:
│ │ │ │ -##  [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C
│ │ │ │ -##  [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8
│ │ │ │ -##  [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8
│ │ │ │ -##  [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C
│ │ │ │ -##  [9] LC_ADDRESS=C               LC_TELEPHONE=C
│ │ │ │ -## [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
│ │ │ │ +##  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
│ │ │ │ +##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
│ │ │ │ +##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
│ │ │ │ +## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
│ │ │ │  ##
│ │ │ │ -## time zone: Europe/Berlin
│ │ │ │ +## time zone: Etc/UTC
│ │ │ │  ## tzcode source: system (glibc)
│ │ │ │  ##
│ │ │ │  ## attached base packages:
│ │ │ │  ## [1] stats     graphics  grDevices utils     datasets  methods   base
│ │ │ │  ##
│ │ │ │  ## other attached packages:
│ │ │ │  ## [1] markdown_2.0 knitr_1.51
│ │ │ │  ##
│ │ │ │  ## loaded via a namespace (and not attached):
│ │ │ │ -##  [1] compiler_4.6.1  cli_3.6.6       tools_4.6.1     pillar_1.11.1
│ │ │ │ -##  [5] otel_0.2.0      glue_1.8.1      vctrs_0.7.3     xfun_0.60
│ │ │ │ -##  [9] lifecycle_1.0.5 rlang_1.3.0     evaluate_1.0.5
│ │ │ │ +## [1] compiler_4.6.1 cli_3.6.6      tools_4.6.1    xfun_0.60      rlang_1.3.0
│ │ │ │ +
│ │ │ │ +## [6] evaluate_1.0.5
│ │ ├── ./usr/lib/R/site-library/ballgown/help/ballgown.rdb
│ │ │ ├── Rscript --vanilla - {}
│ │ │ │ @@ -37,15 +37,15 @@
│ │ │ │          structure("\n", Rd_tag = "TEXT"), structure("  and ", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure("annotated", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure("), and the percent overlap between the two transcripts.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Alyssa Frazee\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("annot = gffReadGR(gtfPath, splitByTranscript=TRUE)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("info = annotate_assembly(assembled=structure(bg)$trans, annotated=annot)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/annotate_assembly.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("info = annotate_assembly(assembled=structure(bg)$trans, annotated=annot)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/annotate_assembly.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  ballgown-class (list) = structure(list(structure(list(structure("Ballgown", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("ballgown-class", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("ballgown-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("Ballgown", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("S4 class for storing and manipulating expression data from assembled\n", Rd_tag = "TEXT"), 
│ │ │ │ @@ -87,15 +87,15 @@
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Alyssa Frazee, Leonardo Collado-Torres, Jeff Leek\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("  data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("  class(bg) #\"ballgown\"\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("  dim(bg@expr$exon)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("  bg@structure$exon\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("  head(bg@indexes$t2g)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("  head(bg@dirs)\n", Rd_tag = "RCODE"), structure("  bg@mergedDate\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("  bg@meas\n", Rd_tag = "RCODE"), structure("  bg@RSEM\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/ballgown-class.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("  bg@meas\n", Rd_tag = "RCODE"), structure("  bg@RSEM\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/ballgown-class.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  ballgown-constructor (list) = structure(list(structure(list(structure("constructor function for ballgown objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("ballgown-constructor", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("ballgown-constructor", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("ballgown", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("constructor function for ballgown objects\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -187,22 +187,22 @@
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Leonardo Collado-Torres, Alyssa Frazee\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure(list(
│ │ │ │          structure(list(structure("ballgownrsem", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure(", for loading RSEM output into a ballgown\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("  object\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("bg = ballgown(dataDir=system.file('extdata', package='ballgown'),\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("    samplePattern='sample')\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("pData(bg) = data.frame(id=sampleNames(bg), group=rep(c(1,0), each=10))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/ballgown-constructor.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("pData(bg) = data.frame(id=sampleNames(bg), group=rep(c(1,0), each=10))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/ballgown-constructor.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  ballgown-package (list) = structure(list(structure(list(structure("The ballgown package for analysis of transcript assemblies", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("ballgown-package", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("ballgown-package", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("ballgownp", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │ -    structure(list(structure("\n", Rd_tag = "TEXT"), structure("Super awesome transcript-level expression analysis\n", Rd_tag = "TEXT")), Rd_tag = "\\description")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/ballgown-package.Rd", class = "Rd", meta = list(
│ │ │ │ +    structure(list(structure("\n", Rd_tag = "TEXT"), structure("Super awesome transcript-level expression analysis\n", Rd_tag = "TEXT")), Rd_tag = "\\description")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/ballgown-package.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "package", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  ballgownrsem (list) = structure(list(structure(list(structure("load RSEM data into a ballgown object", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("ballgownrsem", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("ballgownrsem", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Loads results of rsem-calculate-expression into a ballgown\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("  object for easy visualization, processing, and statistical testing\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -299,28 +299,28 @@
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure(list(
│ │ │ │          structure(list(structure("ballgown", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure(" for reading Cufflinks/Tablemaker output\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("dataDir = system.file('extdata', package='ballgown')\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("gtf = file.path(dataDir, 'hg19_genes_small.gtf.gz')\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("rsemobj = ballgownrsem(dir=dataDir, samples=c('tiny', 'tiny2'), gtf=gtf,\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("    bamout='none', zipped=TRUE)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("rsemobj\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/ballgownrsem.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("rsemobj\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/ballgownrsem.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  bg (list) = structure(list(structure(list(structure("Toy ballgown object", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("bg", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("bg", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Small ballgown object created with simulated toy data, for\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("  demonstration purposes\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("a ", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure("ballgown", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(" object: 100 transcripts, 633 exons, 536 introns\n", Rd_tag = "TEXT")), Rd_tag = "\\format"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Alyssa Frazee\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("bg\n", Rd_tag = "RCODE"), structure("# ballgown instance with 100 transcripts and 20 samples\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/bg.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("bg\n", Rd_tag = "RCODE"), structure("# ballgown instance with 100 transcripts and 20 samples\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/bg.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "data", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  checkAssembledTx (list) = structure(list(structure(list(structure("plot annotated and assembled transcripts together", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("checkAssembledTx", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("checkAssembledTx", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("plot annotated and assembled transcripts together\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("checkAssembledTx(\n", Rd_tag = "RCODE"), 
│ │ │ │ @@ -357,15 +357,15 @@
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plots annotated transcripts on the bottom panel (shaded in gray) and\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("  assembled transcripts on the top panel (shaded with diagonal lines).\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Alyssa Frazee\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure(list(
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("annot = gffReadGR(gtfPath, splitByTranscript=TRUE)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("data(bg)\n", Rd_tag = "RCODE"), structure("checkAssembledTx(annotated=annot, assembled=structure(bg)$trans, ind=4)\n", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/checkAssembledTx.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/checkAssembledTx.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  clusterTranscripts (list) = structure(list(structure(list(structure("group a gene's assembled transcripts into clusters", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("clusterTranscripts", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("clusterTranscripts", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("group a gene's assembled transcripts into clusters\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("clusterTranscripts(gene, gown, k = NULL, method = c(\"hclust\", \"kmeans\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │ @@ -404,15 +404,15 @@
│ │ │ │          structure(", ", Rd_tag = "TEXT"), structure(list(structure(list(
│ │ │ │              structure("kmeans", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure(", \n", Rd_tag = "TEXT"), structure("  ", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure(list(structure("plotLatentTranscripts", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure(" for visualizing the transcript clusters\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("clusterTranscripts('XLOC_000454', bg, k=2, method='kmeans')\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("# transcripts 1294 and 1301 cluster together, 91% variation explained.\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/clusterTranscripts.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("# transcripts 1294 and 1301 cluster together, 91% variation explained.\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/clusterTranscripts.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  collapseTranscripts (list) = structure(list(structure(list(structure("cluster a gene's transcripts and calculate cluster-level expression", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("collapseTranscripts", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("collapseTranscripts", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("cluster a gene's transcripts and calculate cluster-level expression\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("collapseTranscripts(\n", Rd_tag = "RCODE"), 
│ │ │ │ @@ -488,15 +488,15 @@
│ │ │ │          structure(", \n", Rd_tag = "TEXT"), structure("   ", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure(list(structure("clusterTranscripts", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure(", ", Rd_tag = "TEXT"), structure(list(structure(list(
│ │ │ │              structure("plotLatentTranscripts", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("collapseTranscripts(bg, gene='XLOC_000454', meas='FPKM', method='kmeans')\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/collapseTranscripts.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/collapseTranscripts.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  contains (list) = structure(list(structure(list(structure("determine if one set of GRanges fully contains any of another set of GRanges", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("contains", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("contains", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("determine if one set of GRanges fully contains any of another set of GRanges\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("contains(transcripts, cds)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │ @@ -530,15 +530,15 @@
│ │ │ │          structure(").\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Alyssa Frazee\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("## pretend this annotation is coding sequence:\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("annot = gffReadGR(gtfPath, splitByTranscript=TRUE)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("data(bg)\n", Rd_tag = "RCODE"), structure("results = contains(structure(bg)$trans, annot)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("# results is a boolean vector\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("sum(results) #61\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/contains.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("sum(results) #61\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/contains.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  dirs (list) = structure(list(structure(list(structure("extract paths to tablemaker output", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("dirs", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("dirs", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("dirs,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("extract paths to tablemaker output\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -546,15 +546,15 @@
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure(list(list(
│ │ │ │              structure("dirs", Rd_tag = "TEXT")), list(structure("ballgown", Rd_tag = "TEXT"))), Rd_tag = "\\S4method"), 
│ │ │ │          structure("(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure(list(
│ │ │ │          list(structure("x", Rd_tag = "TEXT")), list(structure("a ballgown object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("dirs(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/dirs.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("dirs(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/dirs.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  eexpr (list) = structure(list(structure(list(structure("extract exon-level expression measurements from ballgown objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("eexpr", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("eexpr", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("eexpr,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("extract exon-level expression measurements from ballgown objects\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -578,15 +578,15 @@
│ │ │ │          structure(", or \n", Rd_tag = "TEXT"), structure("  ", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure("x@RSEM", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(" is TRUE, a data frame is returned, containing all\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("  measurements and location information.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("exon_rcount_matrix = eexpr(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("exon_ucount_matrix = eexpr(bg, 'ucount')\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("exon_data_frame = eexpr(bg, 'all')\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/eexpr.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("exon_data_frame = eexpr(bg, 'all')\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/eexpr.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  expr (list) = structure(list(structure(list(structure("extract expression components from ballgown objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("expr", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("expr", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("expr,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("extract expression components from ballgown objects\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -611,15 +611,15 @@
│ │ │ │              structure("eexpr", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure(", \n", Rd_tag = "TEXT"), structure("  ", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure(list(structure("iexpr", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("names(expr(bg))\n", Rd_tag = "RCODE"), structure("class(expr(bg))\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("dim(expr(bg)$exon)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/expr.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/expr.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  expr-replace (list) = structure(list(structure(list(structure("Replacement method for expr slot in ballgown objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("expr<-", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("expr<-", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("expr<-,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Replacement method for expr slot in ballgown objects\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -634,15 +634,15 @@
│ │ │ │              list(structure("the updated value for ", Rd_tag = "TEXT"), 
│ │ │ │                  structure(list(structure("expr(x)", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │                  structure(" or a subcomponent", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("n = ncol(bg@expr$trans)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("#multiply all transcript expression measurements by 10:\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("bg@expr$trans[,11:n] = 10*bg@expr$trans[11:n] \n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/expr-replace.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("bg@expr$trans[,11:n] = 10*bg@expr$trans[11:n] \n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/expr-replace.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  exprfilter (list) = structure(list(structure(list(structure("subset ballgown objects using an expression filter", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("exprfilter", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("exprfilter", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Create a new ballgown object containing only transcripts passing\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("  a mean expression filter\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -670,15 +670,15 @@
│ │ │ │          structure(" across all samples.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure(list(
│ │ │ │          structure(list(structure("subset", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("  data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("  # make a ballgown object containing only transcripts with mean FPKM > 100:\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("  over100 = exprfilter(bg, cutoff=100)  \n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/exprfilter.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/exprfilter.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  geneIDs (list) = structure(list(structure(list(structure("get gene IDs from a ballgown object", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("geneIDs", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("geneIDs", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("geneIDs,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("get gene IDs from a ballgown object\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -695,15 +695,15 @@
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("named vector of gene IDs included in the ballgown object. If object \n", Rd_tag = "TEXT"), 
│ │ │ │          structure("was created using Tablemaker, these gene IDs will be of the form \"XLOC_*\".\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("Vector is named and ordered by corresponding numeric transcript ID.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure(list(
│ │ │ │          structure(list(structure("geneNames", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("geneIDs(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/geneIDs.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("geneIDs(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/geneIDs.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  geneNames (list) = structure(list(structure(list(structure("get gene names from a ballgown object", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("geneNames", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("geneNames", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("geneNames,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("get gene names from a ballgown object\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -732,15 +732,15 @@
│ │ │ │          structure("# this is a de novo assembly, so it does not contain gene info as it stands\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("# but we can add it:\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("annot = system.file('extdata', 'annot.gtf.gz', package='ballgown')\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("gnames = getGenes(annot, structure(bg)$trans, UCSC=FALSE)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("gnames_first = lapply(gnames, function(x) x[1]) #just take 1 overlapping gene\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("expr(bg)$trans$gene_name = gnames_first\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("# now we can extract these gene names:\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("geneNames(bg)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/geneNames.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("geneNames(bg)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/geneNames.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  getAttributeField (list) = structure(list(structure(list(structure("extract a specific field of the \"attributes\" column of a data frame created \n", Rd_tag = "TEXT"), 
│ │ │ │      structure("from a GTF/GFF file", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("getAttributeField", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("getAttributeField", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("extract a specific field of the \"attributes\" column of a data frame created \n", Rd_tag = "TEXT"), 
│ │ │ │ @@ -766,15 +766,15 @@
│ │ │ │          structure(" for creating a data frame from a GTF/GFF file,\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("  and ", Rd_tag = "TEXT"), structure(list(
│ │ │ │              structure("http://useast.ensembl.org/info/website/upload/gff.html", Rd_tag = "VERB")), Rd_tag = "\\url"), 
│ │ │ │          structure(" for\n", Rd_tag = "TEXT"), structure("  specifics of the GFF/GTF file format.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("gffdata = gffRead(gtfPath)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("gffdata$transcriptID = getAttributeField(gffdata$attributes, \n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("  field = \"transcript_id\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/getAttributeField.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("  field = \"transcript_id\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/getAttributeField.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  getGenes (list) = structure(list(structure(list(structure("label assembled transcripts with gene names", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("getGenes", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("getGenes", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("label assembled transcripts with gene names\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("getGenes(gtf, assembled, UCSC = TRUE, attribute = \"gene_id\")\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │ @@ -815,15 +815,15 @@
│ │ │ │          structure(", providing the name(s) of the gene(s) that overlaps each\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("  transcript in ", Rd_tag = "TEXT"), structure(list(
│ │ │ │              structure("assembled", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Alyssa Frazee, Andrew Jaffe\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("geneoverlaps = getGenes(gtfPath, structure(bg)$trans, UCSC=FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/getGenes.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("geneoverlaps = getGenes(gtfPath, structure(bg)$trans, UCSC=FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/getGenes.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  gexpr (list) = structure(list(structure(list(structure("extract gene-level expression measurements from ballgown objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("gexpr", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("gexpr", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("gexpr,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("For objects created with Cufflinks/Tablemaker, gene-level measurements are \n", Rd_tag = "TEXT"), 
│ │ │ │ @@ -835,15 +835,15 @@
│ │ │ │              structure("gexpr", Rd_tag = "TEXT")), list(structure("ballgown", Rd_tag = "TEXT"))), Rd_tag = "\\S4method"), 
│ │ │ │          structure("(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure(list(
│ │ │ │          list(structure("x", Rd_tag = "TEXT")), list(structure("a ballgown object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("gene-by-sample matrix containing per-sample gene measurements.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("gene_matrix = gexpr(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/gexpr.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("gene_matrix = gexpr(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/gexpr.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  gffRead (list) = structure(list(structure(list(structure("read in GTF/GFF file as a data frame", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("gffRead", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("gffRead", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("read in GTF/GFF file as a data frame\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("gffRead(gffFile, nrows = -1, verbose = FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │ @@ -863,15 +863,15 @@
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure(list(
│ │ │ │          structure(list(structure("getAttributeField", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure(" to extract data from \"attributes\" \n", Rd_tag = "TEXT"), 
│ │ │ │          structure(" column; ", Rd_tag = "TEXT"), structure(list(
│ │ │ │              structure("http://useast.ensembl.org/info/website/upload/gff.html", Rd_tag = "VERB")), Rd_tag = "\\url"), 
│ │ │ │          structure(" for\n", Rd_tag = "TEXT"), structure("  more information on the GTF/GFF file format.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("annot = gffRead(gtfPath)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/gffRead.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("annot = gffRead(gtfPath)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/gffRead.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  gffReadGR (list) = structure(list(structure(list(structure("read in gtf file as GRanges object", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("gffReadGR", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("gffReadGR", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("(very) light wrapper for rtracklayer::import\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("gffReadGR(\n", Rd_tag = "RCODE"), 
│ │ │ │ @@ -947,15 +947,15 @@
│ │ │ │          structure("/", Rd_tag = "TEXT"), structure(list(structure("GRangesList", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(" object.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("# read in exons as GRanges:\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("annotgr = gffReadGR(gtfPath)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("# read in groups of exons as transcripts, in GRangesList:\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("transcripts_grl = gffReadGR(gtfPath, splitByTranscript=TRUE)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/gffReadGR.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/gffReadGR.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  hideOutput (NULL) = NULL
│ │ │ │  
│ │ │ │  iexpr (list) = structure(list(structure(list(structure("extract transcript-level expression measurements from ballgown objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("iexpr", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("iexpr", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │ @@ -978,15 +978,15 @@
│ │ │ │          structure(") supporting each intron, in each sample. If\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("  ", Rd_tag = "TEXT"), structure(list(structure("meas", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(" is ", Rd_tag = "TEXT"), structure(list(structure("\"all\"", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(", a data frame is returned, containing all\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("  measurements and location information.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("intron_rcount_matrix = iexpr(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("intron_data_frame = iexpr(bg, 'all')\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/iexpr.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("intron_data_frame = iexpr(bg, 'all')\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/iexpr.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  indexes (list) = structure(list(structure(list(structure("extract the indexes from ballgown objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("indexes", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("indexes", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("indexes,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("extract the indexes from ballgown objects\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -1016,15 +1016,15 @@
│ │ │ │          structure(list(structure("pData", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(" are described in ", Rd_tag = "TEXT"), structure(list(
│ │ │ │              structure("?ballgown", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("names(indexes(bg))\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("class(indexes(bg))\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("head(indexes(bg)$t2g)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/indexes.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("head(indexes(bg)$t2g)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/indexes.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  indexes-replace (list) = structure(list(structure(list(structure("Replace method for indexes slot in ballgown objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("indexes<-", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("indexes<-", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("indexes<-,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Replace method for indexes slot in ballgown objects\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -1038,15 +1038,15 @@
│ │ │ │          structure(list(list(structure("value", Rd_tag = "TEXT")), 
│ │ │ │              list(structure("the updated value for ", Rd_tag = "TEXT"), 
│ │ │ │                  structure(list(structure("indexes(x)", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │                  structure(" or a subcomponent", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("indexes(bg)$bamfiles = paste0('/path/to/bamfolder/', \n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("  sampleNames(bg), '_accepted_hits.bam')\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/indexes-replace.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("  sampleNames(bg), '_accepted_hits.bam')\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/indexes-replace.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  last (list) = structure(list(structure(list(structure("get the last element", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("last", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("last", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("get the last element\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("last(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │ @@ -1057,15 +1057,15 @@
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("this function is made of several thousand lines of complex code,\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("   so be sure to read it carefully.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("the last element of ", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure("x", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Alyssa Frazee\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), 
│ │ │ │ -    structure(list(structure("\n", Rd_tag = "RCODE"), structure("last(c('h', 'e', 'l', 'l', 'o'))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/last.Rd", class = "Rd", meta = list(
│ │ │ │ +    structure(list(structure("\n", Rd_tag = "RCODE"), structure("last(c('h', 'e', 'l', 'l', 'o'))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/last.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  mergedDate (list) = structure(list(structure(list(structure("extract package version & creation date from ballgown object", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("mergedDate", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("mergedDate", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("mergedDate,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("extract package version & creation date from ballgown object\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -1073,15 +1073,15 @@
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure(list(list(
│ │ │ │              structure("mergedDate", Rd_tag = "TEXT")), list(structure("ballgown", Rd_tag = "TEXT"))), Rd_tag = "\\S4method"), 
│ │ │ │          structure("(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure(list(
│ │ │ │          list(structure("x", Rd_tag = "TEXT")), list(structure("a ballgown object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("mergedDate(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/mergedDate.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("mergedDate(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/mergedDate.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  pData (list) = structure(list(structure(list(structure("extract phenotype data from a ballgown object", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("pData", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("pData", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("pData,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("extract phenotype data from a ballgown object\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -1090,15 +1090,15 @@
│ │ │ │              structure("pData", Rd_tag = "TEXT")), list(structure("ballgown", Rd_tag = "TEXT"))), Rd_tag = "\\S4method"), 
│ │ │ │          structure("(object)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure(list(
│ │ │ │          list(structure("object", Rd_tag = "TEXT")), list(structure("a ballgown object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("sample-by-phenotype data frame\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("pData(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/pData.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("pData(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/pData.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  pData-replace (list) = structure(list(structure(list(structure("Replacement method for pData slot in ballgown objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("pData<-", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("pData<-", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("pData<-,ballgown,ANY-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Replacement method for pData slot in ballgown objects\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -1113,15 +1113,15 @@
│ │ │ │              list(structure("the updated value for ", Rd_tag = "TEXT"), 
│ │ │ │                  structure(list(structure("pData(x)", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │                  structure(".", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("# add \"timepoint\" covariate to ballgown object:\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("data(bg) # already contains pData\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("pData(bg) = data.frame(pData(bg), timepoint=rep(1:10, 2))\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("head(pData(bg))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/pData-replace.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("head(pData(bg))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/pData-replace.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  pctOverlap (list) = structure(list(structure(list(structure("calculate percent overlap between two GRanges objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("pctOverlap", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("pctOverlap", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("calculate percent overlap between two GRanges objects\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("pctOverlap(tx1, tx2)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │ @@ -1150,15 +1150,15 @@
│ │ │ │          structure(list(structure("tx1", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(" and ", Rd_tag = "TEXT"), structure(list(structure("tx2", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Alyssa Frazee\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("annot_grl = gffReadGR(gtfPath, splitByTranscript=TRUE)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("pctOverlap(structure(bg)$trans[[2]], annot_grl[[369]]) #79.9%\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/pctOverlap.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("pctOverlap(structure(bg)$trans[[2]], annot_grl[[369]]) #79.9%\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/pctOverlap.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  plotLatentTranscripts (list) = structure(list(structure(list(structure("cluster assembled transcripts and plot the results", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("plotLatentTranscripts", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("plotLatentTranscripts", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("This is an experimental, first-pass function that clusters assembled \n", Rd_tag = "TEXT"), 
│ │ │ │          structure("transcripts based on their overlap percentage, then plots and colors the \n", Rd_tag = "TEXT"), 
│ │ │ │ @@ -1241,15 +1241,15 @@
│ │ │ │          structure(list(structure("clusterTranscripts", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure(", ", Rd_tag = "TEXT"), structure(list(structure(list(
│ │ │ │              structure("plotTranscripts", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure(list(
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("plotLatentTranscripts('XLOC_000454', bg, method='kmeans', k=2)\n", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/plotLatentTranscripts.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/plotLatentTranscripts.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  plotMeans (list) = structure(list(structure(list(structure("visualize transcript abundance by group", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("plotMeans", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("plotMeans", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("visualize transcript abundance by group\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("plotMeans(\n", Rd_tag = "RCODE"), 
│ │ │ │ @@ -1328,15 +1328,15 @@
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure(list(
│ │ │ │          structure(list(structure("plotTranscripts", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure(list(
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("plotMeans('XLOC_000454', bg, groupvar='group', meas='FPKM',\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("  colorby='transcript')\n", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/plotMeans.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/plotMeans.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  plotTranscripts (list) = structure(list(structure(list(structure("visualize structure of assembled transcripts", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("plotTranscripts", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("plotTranscripts", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("visualize structure of assembled transcripts\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("plotTranscripts(\n", Rd_tag = "RCODE"), 
│ │ │ │ @@ -1453,15 +1453,15 @@
│ │ │ │          structure("    colorby='transcript', \n", Rd_tag = "RCODE"), 
│ │ │ │          structure("    main='transcripts from gene XLOC_000454: sample 12, FPKM')\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("# plot one gene for many samples:\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("plotTranscripts('XLOC_000454', bg, \n", Rd_tag = "RCODE"), 
│ │ │ │          structure("    samples=c('sample01', 'sample06', 'sample12', 'sample19'), \n", Rd_tag = "RCODE"), 
│ │ │ │          structure("    meas='FPKM', colorby='transcript')\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/plotTranscripts.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/plotTranscripts.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  safeDeparse (closure) = function (obj) 
│ │ │ │  {
│ │ │ │      tryCatch({
│ │ │ │          deparse(obj)
│ │ │ │      }, error = function(e) {
│ │ │ │ @@ -1486,15 +1486,15 @@
│ │ │ │          structure(list(structure("x", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(". If ", Rd_tag = "TEXT"), structure(list(structure("pData", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(" exists, samples in\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("its rows correspond to samples in ", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(structure("sampleNames(x)", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(" (in order).\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("sampleNames(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/sampleNames.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("sampleNames(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/sampleNames.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  seqnames (list) = structure(list(structure(list(structure("get sequence (chromosome) names from ballgown object", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("seqnames", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("seqnames", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("seqnames,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("get sequence (chromosome) names from ballgown object\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -1504,15 +1504,15 @@
│ │ │ │          structure("(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure(list(
│ │ │ │          list(structure("x", Rd_tag = "TEXT")), list(structure("a ballgown object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("vector of sequence (i.e., chromosome) names included in the \n", Rd_tag = "TEXT"), 
│ │ │ │          structure("ballgown object\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("seqnames(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/seqnames.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("seqnames(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/seqnames.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  stattest (list) = structure(list(structure(list(structure("statistical tests for differential expression in ballgown", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("stattest", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("stattest", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Test each transcript, gene, exon, or intron in a ballgown object for \n", Rd_tag = "TEXT"), 
│ │ │ │          structure("differential expression, using comparisons of linear models.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -1785,15 +1785,15 @@
│ │ │ │          structure("set.seed(43)\n", Rd_tag = "RCODE"), structure("sex = sample(c('M','F'), size=nrow(pData(bg)), replace=TRUE)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("age = sample(21:52, size=nrow(pData(bg)), replace=TRUE)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("### create design matrices:\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("mod = model.matrix(~ sex + age + pData(bg)$group + pData(bg)$time)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("mod0 = model.matrix(~ pData(bg)$group + pData(bg)$time)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("### build model: \n", Rd_tag = "RCODE"), 
│ │ │ │          structure("adjusted_results = stattest(bg, feature='transcript', meas='FPKM', \n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("  mod0=mod0, mod=mod)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/stattest.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("  mod0=mod0, mod=mod)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/stattest.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  structure (list) = structure(list(structure(list(structure("extract structure components from ballgown objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("structure", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("structure", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("structure,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("extract structure components from ballgown objects\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -1819,15 +1819,15 @@
│ │ │ │          structure(" object, where each ", Rd_tag = "TEXT"), structure(list(
│ │ │ │              structure("GRanges", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(" element is a set of \n", Rd_tag = "TEXT"), 
│ │ │ │          structure(" exons representing a transcript.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("names(structure(bg))\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("class(structure(bg))\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("structure(bg)$exon\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/structure.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("structure(bg)$exon\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/structure.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  subset (list) = structure(list(structure(list(structure("subset ballgown objects to specific samples or genomic locations", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("subset", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("subset", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("subset,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("subset ballgown objects to specific samples or genomic locations\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -1873,15 +1873,15 @@
│ │ │ │              structure("cond", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("Alyssa Frazee\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("bg_twogenes = subset(bg, \"gene_id=='XLOC_000454' | gene_id=='XLOC_000024'\")\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("bg_twogenes \n", Rd_tag = "RCODE"), structure("# ballgown instance with 4 assembled transcripts and 20 samples\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("bg_group0 = subset(bg, \"group == 0\", genomesubset=FALSE)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("bg_group0 \n", Rd_tag = "RCODE"), structure("# ballgown instance with 100 assembled transcripts and 10 samples\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/subset.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("bg_group0 \n", Rd_tag = "RCODE"), structure("# ballgown instance with 100 assembled transcripts and 10 samples\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/subset.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  tGene (list) = structure(list(structure(list(structure("Connect a transcript to its gene", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("tGene", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("tGene", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("find the gene to which a transcript belongs\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("tGene(bg, transcript, tid = TRUE, gid = TRUE, warnme = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │ @@ -1930,15 +1930,15 @@
│ │ │ │                  structure("were included when ", Rd_tag = "TEXT"), 
│ │ │ │                  structure(list(structure("bg", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │                  structure(" was created.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("  data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("  tGene(bg, 10)\n", Rd_tag = "RCODE"), structure("  tGene(bg, 'TCONS_00000010', tid=FALSE)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("  tGene(bg, 10, gid=FALSE) #empty: no gene names included in bg.\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/tGene.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/tGene.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  texpr (list) = structure(list(structure(list(structure("extract transcript-level expression measurements from ballgown objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("texpr", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("texpr", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("texpr,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("extract transcript-level expression measurements from ballgown objects\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -1958,15 +1958,15 @@
│ │ │ │          structure("). If ", Rd_tag = "TEXT"), structure(list(
│ │ │ │              structure("meas", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(" is ", Rd_tag = "TEXT"), structure(list(structure("\"all\"", Rd_tag = "RCODE")), Rd_tag = "\\code"), 
│ │ │ │          structure(", a data frame is returned, \n", Rd_tag = "TEXT"), 
│ │ │ │          structure("  containing all measurements and location information.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("transcript_fpkm_matrix = texpr(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("transcript_data_frame = texpr(bg, 'all')\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/texpr.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("transcript_data_frame = texpr(bg, 'all')\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/texpr.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  transcriptIDs (list) = structure(list(structure(list(structure("get numeric transcript IDs from a ballgown object", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("transcriptIDs", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("transcriptIDs", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("transcriptIDs,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("get numeric transcript IDs from a ballgown object\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -1976,15 +1976,15 @@
│ │ │ │              structure("ballgown", Rd_tag = "TEXT"))), Rd_tag = "\\S4method"), 
│ │ │ │          structure("(x)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure(list(
│ │ │ │          list(structure("x", Rd_tag = "TEXT")), list(structure("a ballgown object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("vector of numeric transcript IDs included in the ballgown object\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("transcriptIDs(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/transcriptIDs.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("transcriptIDs(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/transcriptIDs.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  transcriptNames (list) = structure(list(structure(list(structure("get transcript names from a ballgown object", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("transcriptNames", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("transcriptNames", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("transcriptNames,ballgown-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("get transcript names from a ballgown object\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │ @@ -1997,15 +1997,15 @@
│ │ │ │          list(structure("x", Rd_tag = "TEXT")), list(structure("a ballgown object", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("vector of transcript names included in the ballgown object. If object\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("was created using Cufflinks/Tablemaker, these transcript names will be of the\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("form \"TCONS_*\". Return vector is named and ordered by corresponding numeric\n", Rd_tag = "TEXT"), 
│ │ │ │          structure("transcript ID.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │ -        structure("transcriptNames(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/transcriptNames.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("transcriptNames(bg)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/transcriptNames.Rd", class = "Rd", meta = list(
│ │ │ │      docType = "methods", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ │ │  
│ │ │ │  writeFiles (list) = structure(list(structure(list(structure("write files to disk from ballgown object", Rd_tag = "TEXT")), Rd_tag = "\\title"), 
│ │ │ │      structure(list(structure("writeFiles", Rd_tag = "VERB")), Rd_tag = "\\name"), 
│ │ │ │      structure(list(structure("writeFiles", Rd_tag = "VERB")), Rd_tag = "\\alias"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "TEXT"), structure("create tablemaker-like files on disk from a ballgown object\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure("writeFiles(gown, dataDir)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), 
│ │ │ │ @@ -2014,10 +2014,10 @@
│ │ │ │          structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), 
│ │ │ │          structure(list(list(structure("dataDir", Rd_tag = "TEXT")), 
│ │ │ │              list(structure("top-level directory for sample-specific folders", Rd_tag = "TEXT"))), Rd_tag = "\\item"), 
│ │ │ │          structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), 
│ │ │ │      structure(list(structure("\n", Rd_tag = "RCODE"), structure(list(
│ │ │ │          structure("\n", Rd_tag = "RCODE"), structure("  data(bg)\n", Rd_tag = "RCODE"), 
│ │ │ │          structure("  writeFiles(bg, dataDir=getwd())\n", Rd_tag = "RCODE")), Rd_tag = "\\donttest"), 
│ │ │ │ -        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-ballgown/man/writeFiles.Rd", class = "Rd", meta = list(
│ │ │ │ +        structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/writeFiles.Rd", class = "Rd", meta = list(
│ │ │ │      docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L)
│ │ ├── ./usr/lib/R/site-library/ballgown/help/ballgown.rdx
│ │ │ ├── ballgown.rdx-content
│ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}
│ │ │ │ │ @@ -1,265 +1,265 @@
│ │ │ │ │  $variables
│ │ │ │ │  $variables$annotate_assembly
│ │ │ │ │ -[1]  285 1886
│ │ │ │ │ +[1]  294 1900
│ │ │ │ │  
│ │ │ │ │  $variables$`ballgown-class`
│ │ │ │ │ -[1] 2447 2067
│ │ │ │ │ +[1] 2479 2080
│ │ │ │ │  
│ │ │ │ │  $variables$`ballgown-constructor`
│ │ │ │ │ -[1] 4795 3749
│ │ │ │ │ +[1] 4849 3764
│ │ │ │ │  
│ │ │ │ │  $variables$`ballgown-package`
│ │ │ │ │ -[1] 8824  569
│ │ │ │ │ +[1] 8902  585
│ │ │ │ │  
│ │ │ │ │  $variables$ballgownrsem
│ │ │ │ │ -[1] 9667 3725
│ │ │ │ │ +[1] 9772 3740
│ │ │ │ │  
│ │ │ │ │  $variables$bg
│ │ │ │ │ -[1] 13663   836
│ │ │ │ │ +[1] 13794   852
│ │ │ │ │  
│ │ │ │ │  $variables$checkAssembledTx
│ │ │ │ │ -[1] 14784  1935
│ │ │ │ │ +[1] 14941  1948
│ │ │ │ │  
│ │ │ │ │  $variables$clusterTranscripts
│ │ │ │ │ -[1] 17003  2098
│ │ │ │ │ +[1] 17183  2114
│ │ │ │ │  
│ │ │ │ │  $variables$collapseTranscripts
│ │ │ │ │ -[1] 19386  2887
│ │ │ │ │ +[1] 19591  2900
│ │ │ │ │  
│ │ │ │ │  $variables$contains
│ │ │ │ │ -[1] 22548  1807
│ │ │ │ │ +[1] 22776  1823
│ │ │ │ │  
│ │ │ │ │  $variables$dirs
│ │ │ │ │ -[1] 24627   830
│ │ │ │ │ +[1] 24883   847
│ │ │ │ │  
│ │ │ │ │  $variables$eexpr
│ │ │ │ │ -[1] 25733  1413
│ │ │ │ │ +[1] 26016  1427
│ │ │ │ │  
│ │ │ │ │  $variables$`expr-replace`
│ │ │ │ │ -[1] 27426  1106
│ │ │ │ │ +[1] 27733  1122
│ │ │ │ │  
│ │ │ │ │  $variables$expr
│ │ │ │ │ -[1] 28805  1405
│ │ │ │ │ +[1] 29140  1420
│ │ │ │ │  
│ │ │ │ │  $variables$exprfilter
│ │ │ │ │ -[1] 30489  1531
│ │ │ │ │ +[1] 30847  1546
│ │ │ │ │  
│ │ │ │ │  $variables$geneIDs
│ │ │ │ │ -[1] 32297  1274
│ │ │ │ │ +[1] 32679  1287
│ │ │ │ │  
│ │ │ │ │  $variables$geneNames
│ │ │ │ │ -[1] 33848  1776
│ │ │ │ │ +[1] 34254  1790
│ │ │ │ │  
│ │ │ │ │  $variables$getAttributeField
│ │ │ │ │ -[1] 35905  1647
│ │ │ │ │ +[1] 36335  1661
│ │ │ │ │  
│ │ │ │ │  $variables$getGenes
│ │ │ │ │ -[1] 37828  2083
│ │ │ │ │ +[1] 38283  2098
│ │ │ │ │  
│ │ │ │ │  $variables$gexpr
│ │ │ │ │ -[1] 40186  1101
│ │ │ │ │ +[1] 40667  1115
│ │ │ │ │  
│ │ │ │ │  $variables$gffRead
│ │ │ │ │ -[1] 41563  1417
│ │ │ │ │ +[1] 42068  1432
│ │ │ │ │  
│ │ │ │ │  $variables$gffReadGR
│ │ │ │ │ -[1] 43257  2789
│ │ │ │ │ +[1] 43787  2803
│ │ │ │ │  
│ │ │ │ │  $variables$iexpr
│ │ │ │ │ -[1] 46321  1379
│ │ │ │ │ +[1] 46876  1393
│ │ │ │ │  
│ │ │ │ │  $variables$`indexes-replace`
│ │ │ │ │ -[1] 47983  1081
│ │ │ │ │ +[1] 48562  1096
│ │ │ │ │  
│ │ │ │ │  $variables$indexes
│ │ │ │ │ -[1] 49340  1521
│ │ │ │ │ +[1] 49944  1536
│ │ │ │ │  
│ │ │ │ │  $variables$last
│ │ │ │ │ -[1] 51133  1046
│ │ │ │ │ +[1] 51763  1065
│ │ │ │ │  
│ │ │ │ │  $variables$mergedDate
│ │ │ │ │ -[1] 52457   852
│ │ │ │ │ +[1] 53116   868
│ │ │ │ │  
│ │ │ │ │  $variables$`pData-replace`
│ │ │ │ │ -[1] 53589  1113
│ │ │ │ │ +[1] 54274  1129
│ │ │ │ │  
│ │ │ │ │  $variables$pData
│ │ │ │ │ -[1] 54977   896
│ │ │ │ │ +[1] 55688   912
│ │ │ │ │  
│ │ │ │ │  $variables$pctOverlap
│ │ │ │ │ -[1] 56151  1743
│ │ │ │ │ +[1] 56888  1759
│ │ │ │ │  
│ │ │ │ │  $variables$plotLatentTranscripts
│ │ │ │ │ -[1] 58180  3169
│ │ │ │ │ +[1] 58943  3183
│ │ │ │ │  
│ │ │ │ │  $variables$plotMeans
│ │ │ │ │ -[1] 61627  3105
│ │ │ │ │ +[1] 62414  3118
│ │ │ │ │  
│ │ │ │ │  $variables$plotTranscripts
│ │ │ │ │ -[1] 65015  4202
│ │ │ │ │ +[1] 65824  4215
│ │ │ │ │  
│ │ │ │ │  $variables$sampleNames
│ │ │ │ │ -[1] 69496  1084
│ │ │ │ │ +[1] 70329  1103
│ │ │ │ │  
│ │ │ │ │  $variables$seqnames
│ │ │ │ │ -[1] 70855   926
│ │ │ │ │ +[1] 71718   942
│ │ │ │ │  
│ │ │ │ │  $variables$stattest
│ │ │ │ │ -[1] 72056  8853
│ │ │ │ │ +[1] 72945  8863
│ │ │ │ │  
│ │ │ │ │  $variables$structure
│ │ │ │ │ -[1] 81186  1439
│ │ │ │ │ +[1] 82094  1453
│ │ │ │ │  
│ │ │ │ │  $variables$subset
│ │ │ │ │ -[1] 82900  2382
│ │ │ │ │ +[1] 83831  2396
│ │ │ │ │  
│ │ │ │ │  $variables$tGene
│ │ │ │ │ -[1] 85556  2020
│ │ │ │ │ +[1] 86512  2037
│ │ │ │ │  
│ │ │ │ │  $variables$texpr
│ │ │ │ │ -[1] 87851  1320
│ │ │ │ │ +[1] 88835  1337
│ │ │ │ │  
│ │ │ │ │  $variables$transcriptIDs
│ │ │ │ │ -[1] 89451   903
│ │ │ │ │ +[1] 90461   920
│ │ │ │ │  
│ │ │ │ │  $variables$transcriptNames
│ │ │ │ │ -[1] 90637  1051
│ │ │ │ │ +[1] 91673  1066
│ │ │ │ │  
│ │ │ │ │  $variables$writeFiles
│ │ │ │ │ -[1] 91966   891
│ │ │ │ │ +[1] 93025   911
│ │ │ │ │  
│ │ │ │ │  
│ │ │ │ │  $references
│ │ │ │ │  $references$`env::1`
│ │ │ │ │ -[1]   0 285
│ │ │ │ │ +[1]   0 294
│ │ │ │ │  
│ │ │ │ │  $references$`env::10`
│ │ │ │ │ -[1] 22273   275
│ │ │ │ │ +[1] 22491   285
│ │ │ │ │  
│ │ │ │ │  $references$`env::11`
│ │ │ │ │ -[1] 24355   272
│ │ │ │ │ +[1] 24599   284
│ │ │ │ │  
│ │ │ │ │  $references$`env::12`
│ │ │ │ │ -[1] 25457   276
│ │ │ │ │ +[1] 25730   286
│ │ │ │ │  
│ │ │ │ │  $references$`env::13`
│ │ │ │ │ -[1] 27146   280
│ │ │ │ │ +[1] 27443   290
│ │ │ │ │  
│ │ │ │ │  $references$`env::14`
│ │ │ │ │ -[1] 28532   273
│ │ │ │ │ +[1] 28855   285
│ │ │ │ │  
│ │ │ │ │  $references$`env::15`
│ │ │ │ │ -[1] 30210   279
│ │ │ │ │ +[1] 30560   287
│ │ │ │ │  
│ │ │ │ │  $references$`env::16`
│ │ │ │ │ -[1] 32020   277
│ │ │ │ │ +[1] 32393   286
│ │ │ │ │  
│ │ │ │ │  $references$`env::17`
│ │ │ │ │ -[1] 33571   277
│ │ │ │ │ +[1] 33966   288
│ │ │ │ │  
│ │ │ │ │  $references$`env::18`
│ │ │ │ │ -[1] 35624   281
│ │ │ │ │ +[1] 36044   291
│ │ │ │ │  
│ │ │ │ │  $references$`env::19`
│ │ │ │ │ -[1] 37552   276
│ │ │ │ │ +[1] 37996   287
│ │ │ │ │  
│ │ │ │ │  $references$`env::2`
│ │ │ │ │ -[1] 2171  276
│ │ │ │ │ +[1] 2194  285
│ │ │ │ │  
│ │ │ │ │  $references$`env::20`
│ │ │ │ │ -[1] 39911   275
│ │ │ │ │ +[1] 40381   286
│ │ │ │ │  
│ │ │ │ │  $references$`env::21`
│ │ │ │ │ -[1] 41287   276
│ │ │ │ │ +[1] 41782   286
│ │ │ │ │  
│ │ │ │ │  $references$`env::22`
│ │ │ │ │ -[1] 42980   277
│ │ │ │ │ +[1] 43500   287
│ │ │ │ │  
│ │ │ │ │  $references$`env::23`
│ │ │ │ │ -[1] 46046   275
│ │ │ │ │ +[1] 46590   286
│ │ │ │ │  
│ │ │ │ │  $references$`env::24`
│ │ │ │ │ -[1] 47700   283
│ │ │ │ │ +[1] 48269   293
│ │ │ │ │  
│ │ │ │ │  $references$`env::25`
│ │ │ │ │ -[1] 49064   276
│ │ │ │ │ +[1] 49658   286
│ │ │ │ │  
│ │ │ │ │  $references$`env::26`
│ │ │ │ │ -[1] 50861   272
│ │ │ │ │ +[1] 51480   283
│ │ │ │ │  
│ │ │ │ │  $references$`env::27`
│ │ │ │ │ -[1] 52179   278
│ │ │ │ │ +[1] 52828   288
│ │ │ │ │  
│ │ │ │ │  $references$`env::28`
│ │ │ │ │ -[1] 53309   280
│ │ │ │ │ +[1] 53984   290
│ │ │ │ │  
│ │ │ │ │  $references$`env::29`
│ │ │ │ │ -[1] 54702   275
│ │ │ │ │ +[1] 55403   285
│ │ │ │ │  
│ │ │ │ │  $references$`env::3`
│ │ │ │ │ -[1] 4514  281
│ │ │ │ │ +[1] 4559  290
│ │ │ │ │  
│ │ │ │ │  $references$`env::30`
│ │ │ │ │ -[1] 55873   278
│ │ │ │ │ +[1] 56600   288
│ │ │ │ │  
│ │ │ │ │  $references$`env::31`
│ │ │ │ │ -[1] 57894   286
│ │ │ │ │ +[1] 58647   296
│ │ │ │ │  
│ │ │ │ │  $references$`env::32`
│ │ │ │ │ -[1] 61349   278
│ │ │ │ │ +[1] 62126   288
│ │ │ │ │  
│ │ │ │ │  $references$`env::33`
│ │ │ │ │ -[1] 64732   283
│ │ │ │ │ +[1] 65532   292
│ │ │ │ │  
│ │ │ │ │  $references$`env::34`
│ │ │ │ │ -[1] 69217   279
│ │ │ │ │ +[1] 70039   290
│ │ │ │ │  
│ │ │ │ │  $references$`env::35`
│ │ │ │ │ -[1] 70580   275
│ │ │ │ │ +[1] 71432   286
│ │ │ │ │  
│ │ │ │ │  $references$`env::36`
│ │ │ │ │ -[1] 71781   275
│ │ │ │ │ +[1] 72660   285
│ │ │ │ │  
│ │ │ │ │  $references$`env::37`
│ │ │ │ │ -[1] 80909   277
│ │ │ │ │ +[1] 81808   286
│ │ │ │ │  
│ │ │ │ │  $references$`env::38`
│ │ │ │ │ -[1] 82625   275
│ │ │ │ │ +[1] 83547   284
│ │ │ │ │  
│ │ │ │ │  $references$`env::39`
│ │ │ │ │ -[1] 85282   274
│ │ │ │ │ +[1] 86227   285
│ │ │ │ │  
│ │ │ │ │  $references$`env::4`
│ │ │ │ │ -[1] 8544  280
│ │ │ │ │ +[1] 8613  289
│ │ │ │ │  
│ │ │ │ │  $references$`env::40`
│ │ │ │ │ -[1] 87576   275
│ │ │ │ │ +[1] 88549   286
│ │ │ │ │  
│ │ │ │ │  $references$`env::41`
│ │ │ │ │ -[1] 89171   280
│ │ │ │ │ +[1] 90172   289
│ │ │ │ │  
│ │ │ │ │  $references$`env::42`
│ │ │ │ │ -[1] 90354   283
│ │ │ │ │ +[1] 91381   292
│ │ │ │ │  
│ │ │ │ │  $references$`env::43`
│ │ │ │ │ -[1] 91688   278
│ │ │ │ │ +[1] 92739   286
│ │ │ │ │  
│ │ │ │ │  $references$`env::5`
│ │ │ │ │ -[1] 9393  274
│ │ │ │ │ +[1] 9487  285
│ │ │ │ │  
│ │ │ │ │  $references$`env::6`
│ │ │ │ │ -[1] 13392   271
│ │ │ │ │ +[1] 13512   282
│ │ │ │ │  
│ │ │ │ │  $references$`env::7`
│ │ │ │ │ -[1] 14499   285
│ │ │ │ │ +[1] 14646   295
│ │ │ │ │  
│ │ │ │ │  $references$`env::8`
│ │ │ │ │ -[1] 16719   284
│ │ │ │ │ +[1] 16889   294
│ │ │ │ │  
│ │ │ │ │  $references$`env::9`
│ │ │ │ │ -[1] 19101   285
│ │ │ │ │ +[1] 19297   294
│ │ │ │ │  
│ │ │ │ │  
│ │ │ │ │  $compressed
│ │ │ │ │  [1] TRUE
│ │ ├── ./usr/lib/R/site-library/ballgown/help/paths.rds
│ │ │ ├── paths.rds-content
│ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {}
│ │ │ │ │ @@ -1,45 +1,45 @@
│ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-ballgown/man/annotate_assembly.Rd"    
│ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-ballgown/man/ballgown-class.Rd"       
│ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-ballgown/man/ballgown-constructor.Rd" 
│ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-ballgown/man/ballgown-package.Rd"     
│ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-ballgown/man/ballgownrsem.Rd"         
│ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-ballgown/man/bg.Rd"                   
│ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-ballgown/man/checkAssembledTx.Rd"     
│ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-ballgown/man/clusterTranscripts.Rd"   
│ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-ballgown/man/collapseTranscripts.Rd"  
│ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-ballgown/man/contains.Rd"             
│ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-ballgown/man/dirs.Rd"                 
│ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-ballgown/man/eexpr.Rd"                
│ │ │ │ │ -[13] "/home/moeller/Salsa/r-bioc-ballgown/man/expr-replace.Rd"         
│ │ │ │ │ -[14] "/home/moeller/Salsa/r-bioc-ballgown/man/expr.Rd"                 
│ │ │ │ │ -[15] "/home/moeller/Salsa/r-bioc-ballgown/man/exprfilter.Rd"           
│ │ │ │ │ -[16] "/home/moeller/Salsa/r-bioc-ballgown/man/geneIDs.Rd"              
│ │ │ │ │ -[17] "/home/moeller/Salsa/r-bioc-ballgown/man/geneNames.Rd"            
│ │ │ │ │ -[18] "/home/moeller/Salsa/r-bioc-ballgown/man/getAttributeField.Rd"    
│ │ │ │ │ -[19] "/home/moeller/Salsa/r-bioc-ballgown/man/getGenes.Rd"             
│ │ │ │ │ -[20] "/home/moeller/Salsa/r-bioc-ballgown/man/gexpr.Rd"                
│ │ │ │ │ -[21] "/home/moeller/Salsa/r-bioc-ballgown/man/gffRead.Rd"              
│ │ │ │ │ -[22] "/home/moeller/Salsa/r-bioc-ballgown/man/gffReadGR.Rd"            
│ │ │ │ │ -[23] "/home/moeller/Salsa/r-bioc-ballgown/man/iexpr.Rd"                
│ │ │ │ │ -[24] "/home/moeller/Salsa/r-bioc-ballgown/man/indexes-replace.Rd"      
│ │ │ │ │ -[25] "/home/moeller/Salsa/r-bioc-ballgown/man/indexes.Rd"              
│ │ │ │ │ -[26] "/home/moeller/Salsa/r-bioc-ballgown/man/last.Rd"                 
│ │ │ │ │ -[27] "/home/moeller/Salsa/r-bioc-ballgown/man/mergedDate.Rd"           
│ │ │ │ │ -[28] "/home/moeller/Salsa/r-bioc-ballgown/man/pData-replace.Rd"        
│ │ │ │ │ -[29] "/home/moeller/Salsa/r-bioc-ballgown/man/pData.Rd"                
│ │ │ │ │ -[30] "/home/moeller/Salsa/r-bioc-ballgown/man/pctOverlap.Rd"           
│ │ │ │ │ -[31] "/home/moeller/Salsa/r-bioc-ballgown/man/plotLatentTranscripts.Rd"
│ │ │ │ │ -[32] "/home/moeller/Salsa/r-bioc-ballgown/man/plotMeans.Rd"            
│ │ │ │ │ -[33] "/home/moeller/Salsa/r-bioc-ballgown/man/plotTranscripts.Rd"      
│ │ │ │ │ -[34] "/home/moeller/Salsa/r-bioc-ballgown/man/sampleNames.Rd"          
│ │ │ │ │ -[35] "/home/moeller/Salsa/r-bioc-ballgown/man/seqnames.Rd"             
│ │ │ │ │ -[36] "/home/moeller/Salsa/r-bioc-ballgown/man/stattest.Rd"             
│ │ │ │ │ -[37] "/home/moeller/Salsa/r-bioc-ballgown/man/structure.Rd"            
│ │ │ │ │ -[38] "/home/moeller/Salsa/r-bioc-ballgown/man/subset.Rd"               
│ │ │ │ │ -[39] "/home/moeller/Salsa/r-bioc-ballgown/man/tGene.Rd"                
│ │ │ │ │ -[40] "/home/moeller/Salsa/r-bioc-ballgown/man/texpr.Rd"                
│ │ │ │ │ -[41] "/home/moeller/Salsa/r-bioc-ballgown/man/transcriptIDs.Rd"        
│ │ │ │ │ -[42] "/home/moeller/Salsa/r-bioc-ballgown/man/transcriptNames.Rd"      
│ │ │ │ │ -[43] "/home/moeller/Salsa/r-bioc-ballgown/man/writeFiles.Rd"           
│ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/annotate_assembly.Rd"    
│ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/ballgown-class.Rd"       
│ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/ballgown-constructor.Rd" 
│ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/ballgown-package.Rd"     
│ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/ballgownrsem.Rd"         
│ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/bg.Rd"                   
│ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/checkAssembledTx.Rd"     
│ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/clusterTranscripts.Rd"   
│ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/collapseTranscripts.Rd"  
│ │ │ │ │ +[10] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/contains.Rd"             
│ │ │ │ │ +[11] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/dirs.Rd"                 
│ │ │ │ │ +[12] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/eexpr.Rd"                
│ │ │ │ │ +[13] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/expr-replace.Rd"         
│ │ │ │ │ +[14] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/expr.Rd"                 
│ │ │ │ │ +[15] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/exprfilter.Rd"           
│ │ │ │ │ +[16] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/geneIDs.Rd"              
│ │ │ │ │ +[17] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/geneNames.Rd"            
│ │ │ │ │ +[18] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/getAttributeField.Rd"    
│ │ │ │ │ +[19] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/getGenes.Rd"             
│ │ │ │ │ +[20] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/gexpr.Rd"                
│ │ │ │ │ +[21] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/gffRead.Rd"              
│ │ │ │ │ +[22] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/gffReadGR.Rd"            
│ │ │ │ │ +[23] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/iexpr.Rd"                
│ │ │ │ │ +[24] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/indexes-replace.Rd"      
│ │ │ │ │ +[25] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/indexes.Rd"              
│ │ │ │ │ +[26] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/last.Rd"                 
│ │ │ │ │ +[27] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/mergedDate.Rd"           
│ │ │ │ │ +[28] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/pData-replace.Rd"        
│ │ │ │ │ +[29] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/pData.Rd"                
│ │ │ │ │ +[30] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/pctOverlap.Rd"           
│ │ │ │ │ +[31] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/plotLatentTranscripts.Rd"
│ │ │ │ │ +[32] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/plotMeans.Rd"            
│ │ │ │ │ +[33] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/plotTranscripts.Rd"      
│ │ │ │ │ +[34] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/sampleNames.Rd"          
│ │ │ │ │ +[35] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/seqnames.Rd"             
│ │ │ │ │ +[36] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/stattest.Rd"             
│ │ │ │ │ +[37] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/structure.Rd"            
│ │ │ │ │ +[38] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/subset.Rd"               
│ │ │ │ │ +[39] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/tGene.Rd"                
│ │ │ │ │ +[40] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/texpr.Rd"                
│ │ │ │ │ +[41] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/transcriptIDs.Rd"        
│ │ │ │ │ +[42] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/transcriptNames.Rd"      
│ │ │ │ │ +[43] "/build/reproducible-path/r-bioc-ballgown-2.43.0+dfsg/man/writeFiles.Rd"           
│ │ │ │ │  attr(,"first")
│ │ │ │ │ -[1] 41
│ │ │ │ │ +[1] 58