--- /srv/rebuilderd/tmp/rebuilderdxv76oi/inputs/r-bioc-aroma.light_3.42.0-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdxv76oi/out/r-bioc-aroma.light_3.42.0-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-06 23:46:49.000000 debian-binary │ --rw-r--r-- 0 0 0 2336 2026-08-06 23:46:49.000000 control.tar.xz │ --rw-r--r-- 0 0 0 584272 2026-08-06 23:46:49.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 2316 2026-08-06 23:46:49.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 585620 2026-08-06 23:46:49.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:46:49.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 887 2026-08-06 23:46:49.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 849 2026-08-06 23:46:49.000000 ./control │ │ │ -rw-r--r-- 0 root (0) root (0) 4990 2026-08-06 23:46:49.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,13 @@ │ │ │ Package: r-bioc-aroma.light │ │ │ Version: 3.42.0-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ -Installed-Size: 919 │ │ │ +Installed-Size: 920 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-cran-r.methodss3 (>= 1.7.1), r-cran-r.oo (>= 1.23.0), r-cran-r.utils (>= 2.9.0), r-cran-matrixstats (>= 0.55.0) │ │ │ -Suggests: r-cran-princurve (>= 2.1.4) │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/aroma.light/ │ │ │ Description: BioConductor methods normalization and visualization of microarray data │ │ │ This BioConductor module provides light-weight methods for │ │ │ normalization and visualization of microarray data using only basic R │ │ │ data types. │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -14,26 +14,26 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 1230 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/Meta/links.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1104 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1334 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/Meta/package.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 4148 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 31791 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/NEWS.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/R/aroma.light │ │ │ --rw-r--r-- 0 root (0) root (0) 148260 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/R/aroma.light.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 148268 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/R/aroma.light.rdb │ │ │ -rw-r--r-- 0 root (0) root (0) 1642 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/R/aroma.light.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 631 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/WORDLIST │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/data-ex/ │ │ │ -rw-r--r-- 0 root (0) root (0) 259157 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/data-ex/PMT-RGData.dat │ │ │ -rw-r--r-- 0 root (0) root (0) 64383 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/data-ex/TumorBoost,fracB,exampleData.Rbin │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 4114 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/help/AnIndex │ │ │ -rw-r--r-- 0 root (0) root (0) 1047 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 178122 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/help/aroma.light.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 1151 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/help/aroma.light.rdx │ │ │ --rw-r--r-- 0 root (0) root (0) 584 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 178914 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/help/aroma.light.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 1153 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/help/aroma.light.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 593 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 14991 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/rsp/ │ │ │ -rw-r--r-- 0 root (0) root (0) 39 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/rsp/.rspPlugins │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/rsp/AffineNormalization/ │ │ │ -rw-r--r-- 0 root (0) root (0) 9629 2026-08-06 23:46:49.000000 ./usr/lib/R/site-library/aroma.light/rsp/AffineNormalization/AffineNormalization.html.rsp │ │ ├── ./usr/lib/R/site-library/aroma.light/R/aroma.light.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -21,15 +21,15 @@ │ │ │ │ "imports" = " density = "density", integrate = "integrate", loess = "loess", " │ │ │ │ "imports" = " loess.control = "loess.control", lowess = "lowess", mad = "mad", " │ │ │ │ "imports" = " median = "median", na.omit = "na.omit", predict = "predict", " │ │ │ │ "imports" = " sd = "sd", smooth.spline = "smooth.spline", weighted.mean = "weighted.mean", " │ │ │ │ "imports" = " weights = "weights"), utils = c(getAnywhere = "getAnywhere", " │ │ │ │ "imports" = " packageDescription = "packageDescription"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-aroma.light/debian/r-bioc-aroma.light/usr/lib/R/site-library/aroma.light"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-aroma.light-3.42.0/debian/r-bioc-aroma.light/usr/lib/R/site-library/aroma.light"" │ │ │ │ "spec" = "c(name = "aroma.light", version = "3.42.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/aroma.light/R/aroma.light.rdx │ │ │ ├── aroma.light.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,331 +1,331 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 1114 52 │ │ │ │ │ +[1] 1122 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 1297 52 │ │ │ │ │ +[1] 1305 52 │ │ │ │ │ │ │ │ │ │ $variables$.conflicts.OK │ │ │ │ │ -[1] 1349 42 │ │ │ │ │ +[1] 1357 42 │ │ │ │ │ │ │ │ │ │ $variables$.onAttach │ │ │ │ │ -[1] 1391 375 │ │ │ │ │ +[1] 1399 375 │ │ │ │ │ │ │ │ │ │ $variables$.onLoad │ │ │ │ │ -[1] 1766 398 │ │ │ │ │ +[1] 1774 398 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 2164 56 │ │ │ │ │ +[1] 2172 56 │ │ │ │ │ │ │ │ │ │ $variables$.whichUnique │ │ │ │ │ -[1] 2220 893 │ │ │ │ │ +[1] 2228 893 │ │ │ │ │ │ │ │ │ │ $variables$averageQuantile │ │ │ │ │ -[1] 3113 198 │ │ │ │ │ +[1] 3121 198 │ │ │ │ │ │ │ │ │ │ $variables$averageQuantile.list │ │ │ │ │ -[1] 3311 1572 │ │ │ │ │ +[1] 3319 1572 │ │ │ │ │ │ │ │ │ │ $variables$averageQuantile.matrix │ │ │ │ │ -[1] 4883 1450 │ │ │ │ │ +[1] 4891 1450 │ │ │ │ │ │ │ │ │ │ $variables$backtransformAffine │ │ │ │ │ -[1] 6333 203 │ │ │ │ │ +[1] 6341 203 │ │ │ │ │ │ │ │ │ │ $variables$backtransformAffine.matrix │ │ │ │ │ -[1] 6536 2706 │ │ │ │ │ +[1] 6544 2706 │ │ │ │ │ │ │ │ │ │ $variables$backtransformPrincipalCurve │ │ │ │ │ -[1] 9242 209 │ │ │ │ │ +[1] 9250 209 │ │ │ │ │ │ │ │ │ │ $variables$backtransformPrincipalCurve.matrix │ │ │ │ │ -[1] 9451 3646 │ │ │ │ │ +[1] 9459 3646 │ │ │ │ │ │ │ │ │ │ $variables$backtransformPrincipalCurve.numeric │ │ │ │ │ -[1] 13097 361 │ │ │ │ │ +[1] 13105 361 │ │ │ │ │ │ │ │ │ │ $variables$backtransformXYCurve │ │ │ │ │ -[1] 13458 204 │ │ │ │ │ +[1] 13466 204 │ │ │ │ │ │ │ │ │ │ $variables$backtransformXYCurve.matrix │ │ │ │ │ -[1] 13662 1219 │ │ │ │ │ +[1] 13670 1219 │ │ │ │ │ │ │ │ │ │ $variables$calibrateMultiscan │ │ │ │ │ -[1] 14881 200 │ │ │ │ │ +[1] 14889 200 │ │ │ │ │ │ │ │ │ │ $variables$calibrateMultiscan.matrix │ │ │ │ │ -[1] 15081 3326 │ │ │ │ │ +[1] 15089 3326 │ │ │ │ │ │ │ │ │ │ $variables$callNaiveGenotypes │ │ │ │ │ -[1] 18407 201 │ │ │ │ │ +[1] 18415 201 │ │ │ │ │ │ │ │ │ │ $variables$callNaiveGenotypes.numeric │ │ │ │ │ -[1] 18608 5675 │ │ │ │ │ +[1] 18616 5675 │ │ │ │ │ │ │ │ │ │ $variables$distanceBetweenLines │ │ │ │ │ -[1] 24283 202 │ │ │ │ │ +[1] 24291 202 │ │ │ │ │ │ │ │ │ │ $variables$distanceBetweenLines.default │ │ │ │ │ -[1] 24485 3076 │ │ │ │ │ +[1] 24493 3076 │ │ │ │ │ │ │ │ │ │ $variables$findPeaksAndValleys │ │ │ │ │ -[1] 27561 203 │ │ │ │ │ +[1] 27569 203 │ │ │ │ │ │ │ │ │ │ $variables$findPeaksAndValleys.density │ │ │ │ │ -[1] 27764 1783 │ │ │ │ │ +[1] 27772 1783 │ │ │ │ │ │ │ │ │ │ $variables$findPeaksAndValleys.numeric │ │ │ │ │ -[1] 29547 723 │ │ │ │ │ +[1] 29555 723 │ │ │ │ │ │ │ │ │ │ $variables$fitIWPCA │ │ │ │ │ -[1] 30270 195 │ │ │ │ │ +[1] 30278 195 │ │ │ │ │ │ │ │ │ │ $variables$fitIWPCA.matrix │ │ │ │ │ -[1] 30465 6461 │ │ │ │ │ +[1] 30473 6461 │ │ │ │ │ │ │ │ │ │ $variables$fitNaiveGenotypes │ │ │ │ │ -[1] 36926 201 │ │ │ │ │ +[1] 36934 201 │ │ │ │ │ │ │ │ │ │ $variables$fitNaiveGenotypes.numeric │ │ │ │ │ -[1] 37127 6503 │ │ │ │ │ +[1] 37135 6503 │ │ │ │ │ │ │ │ │ │ $variables$fitPrincipalCurve │ │ │ │ │ -[1] 43630 202 │ │ │ │ │ +[1] 43638 202 │ │ │ │ │ │ │ │ │ │ $variables$fitPrincipalCurve.matrix │ │ │ │ │ -[1] 43832 3226 │ │ │ │ │ +[1] 43840 3226 │ │ │ │ │ │ │ │ │ │ $variables$fitXYCurve │ │ │ │ │ -[1] 47058 195 │ │ │ │ │ +[1] 47066 195 │ │ │ │ │ │ │ │ │ │ $variables$fitXYCurve.matrix │ │ │ │ │ -[1] 47253 5140 │ │ │ │ │ +[1] 47261 5140 │ │ │ │ │ │ │ │ │ │ $variables$iwpca │ │ │ │ │ -[1] 52393 190 │ │ │ │ │ +[1] 52401 190 │ │ │ │ │ │ │ │ │ │ $variables$iwpca.matrix │ │ │ │ │ -[1] 52583 4757 │ │ │ │ │ +[1] 52591 4757 │ │ │ │ │ │ │ │ │ │ $variables$likelihood │ │ │ │ │ -[1] 57340 193 │ │ │ │ │ +[1] 57348 193 │ │ │ │ │ │ │ │ │ │ $variables$likelihood.smooth.spline │ │ │ │ │ -[1] 57533 3265 │ │ │ │ │ +[1] 57541 3265 │ │ │ │ │ │ │ │ │ │ $variables$lines.XYCurveFit │ │ │ │ │ -[1] 60798 671 │ │ │ │ │ +[1] 60806 671 │ │ │ │ │ │ │ │ │ │ $variables$medianPolish │ │ │ │ │ -[1] 61469 196 │ │ │ │ │ +[1] 61477 196 │ │ │ │ │ │ │ │ │ │ $variables$medianPolish.matrix │ │ │ │ │ -[1] 61665 3870 │ │ │ │ │ +[1] 61673 3870 │ │ │ │ │ │ │ │ │ │ $variables$normalizeAffine │ │ │ │ │ -[1] 65535 199 │ │ │ │ │ +[1] 65543 199 │ │ │ │ │ │ │ │ │ │ $variables$normalizeAffine.matrix │ │ │ │ │ -[1] 65734 2599 │ │ │ │ │ +[1] 65742 2599 │ │ │ │ │ │ │ │ │ │ $variables$normalizeAverage │ │ │ │ │ -[1] 68333 199 │ │ │ │ │ +[1] 68341 199 │ │ │ │ │ │ │ │ │ │ $variables$normalizeAverage.list │ │ │ │ │ -[1] 68532 997 │ │ │ │ │ +[1] 68540 997 │ │ │ │ │ │ │ │ │ │ $variables$normalizeAverage.matrix │ │ │ │ │ -[1] 69529 965 │ │ │ │ │ +[1] 69537 965 │ │ │ │ │ │ │ │ │ │ $variables$normalizeCurveFit │ │ │ │ │ -[1] 70494 201 │ │ │ │ │ +[1] 70502 201 │ │ │ │ │ │ │ │ │ │ $variables$normalizeCurveFit.matrix │ │ │ │ │ -[1] 70695 5848 │ │ │ │ │ +[1] 70703 5848 │ │ │ │ │ │ │ │ │ │ $variables$normalizeDifferencesToAverage │ │ │ │ │ -[1] 76543 209 │ │ │ │ │ +[1] 76551 209 │ │ │ │ │ │ │ │ │ │ $variables$normalizeDifferencesToAverage.list │ │ │ │ │ -[1] 76752 1760 │ │ │ │ │ +[1] 76760 1760 │ │ │ │ │ │ │ │ │ │ $variables$normalizeFragmentLength │ │ │ │ │ -[1] 78512 205 │ │ │ │ │ +[1] 78520 205 │ │ │ │ │ │ │ │ │ │ $variables$normalizeFragmentLength.default │ │ │ │ │ -[1] 78717 7022 │ │ │ │ │ +[1] 78725 7022 │ │ │ │ │ │ │ │ │ │ $variables$normalizeLoess │ │ │ │ │ -[1] 85739 198 │ │ │ │ │ +[1] 85747 198 │ │ │ │ │ │ │ │ │ │ $variables$normalizeLoess.matrix │ │ │ │ │ -[1] 85937 324 │ │ │ │ │ +[1] 85945 324 │ │ │ │ │ │ │ │ │ │ $variables$normalizeLowess │ │ │ │ │ -[1] 86261 198 │ │ │ │ │ +[1] 86269 198 │ │ │ │ │ │ │ │ │ │ $variables$normalizeLowess.matrix │ │ │ │ │ -[1] 86459 325 │ │ │ │ │ +[1] 86467 325 │ │ │ │ │ │ │ │ │ │ $variables$normalizeQuantile │ │ │ │ │ -[1] 86784 201 │ │ │ │ │ +[1] 86792 201 │ │ │ │ │ │ │ │ │ │ $variables$normalizeQuantile.default │ │ │ │ │ -[1] 86985 298 │ │ │ │ │ +[1] 86993 298 │ │ │ │ │ │ │ │ │ │ $variables$normalizeQuantileRank │ │ │ │ │ -[1] 87283 204 │ │ │ │ │ +[1] 87291 204 │ │ │ │ │ │ │ │ │ │ $variables$normalizeQuantileRank.list │ │ │ │ │ -[1] 87487 652 │ │ │ │ │ +[1] 87495 652 │ │ │ │ │ │ │ │ │ │ $variables$normalizeQuantileRank.matrix │ │ │ │ │ -[1] 88139 5828 │ │ │ │ │ +[1] 88147 5828 │ │ │ │ │ │ │ │ │ │ $variables$normalizeQuantileRank.numeric │ │ │ │ │ -[1] 93967 2330 │ │ │ │ │ +[1] 93975 2330 │ │ │ │ │ │ │ │ │ │ $variables$normalizeQuantileSpline │ │ │ │ │ -[1] 96297 206 │ │ │ │ │ +[1] 96305 206 │ │ │ │ │ │ │ │ │ │ $variables$normalizeQuantileSpline.list │ │ │ │ │ -[1] 96503 1036 │ │ │ │ │ +[1] 96511 1036 │ │ │ │ │ │ │ │ │ │ $variables$normalizeQuantileSpline.matrix │ │ │ │ │ -[1] 97539 1315 │ │ │ │ │ +[1] 97547 1315 │ │ │ │ │ │ │ │ │ │ $variables$normalizeQuantileSpline.numeric │ │ │ │ │ -[1] 98854 2317 │ │ │ │ │ +[1] 98862 2317 │ │ │ │ │ │ │ │ │ │ $variables$normalizeRobustSpline │ │ │ │ │ -[1] 101171 204 │ │ │ │ │ +[1] 101179 204 │ │ │ │ │ │ │ │ │ │ $variables$normalizeRobustSpline.matrix │ │ │ │ │ -[1] 101375 330 │ │ │ │ │ +[1] 101383 330 │ │ │ │ │ │ │ │ │ │ $variables$normalizeSpline │ │ │ │ │ -[1] 101705 198 │ │ │ │ │ +[1] 101713 198 │ │ │ │ │ │ │ │ │ │ $variables$normalizeSpline.matrix │ │ │ │ │ -[1] 101903 324 │ │ │ │ │ +[1] 101911 324 │ │ │ │ │ │ │ │ │ │ $variables$normalizeTumorBoost │ │ │ │ │ -[1] 102227 202 │ │ │ │ │ +[1] 102235 202 │ │ │ │ │ │ │ │ │ │ $variables$normalizeTumorBoost.numeric │ │ │ │ │ -[1] 102429 5006 │ │ │ │ │ +[1] 102437 5006 │ │ │ │ │ │ │ │ │ │ $variables$pairedAlleleSpecificCopyNumbers │ │ │ │ │ -[1] 107435 214 │ │ │ │ │ +[1] 107443 214 │ │ │ │ │ │ │ │ │ │ $variables$pairedAlleleSpecificCopyNumbers.numeric │ │ │ │ │ -[1] 107649 3791 │ │ │ │ │ +[1] 107657 3791 │ │ │ │ │ │ │ │ │ │ $variables$plotDensity │ │ │ │ │ -[1] 111440 196 │ │ │ │ │ +[1] 111448 196 │ │ │ │ │ │ │ │ │ │ $variables$plotDensity.data.frame │ │ │ │ │ -[1] 111636 463 │ │ │ │ │ +[1] 111644 463 │ │ │ │ │ │ │ │ │ │ $variables$plotDensity.density │ │ │ │ │ -[1] 112099 450 │ │ │ │ │ +[1] 112107 450 │ │ │ │ │ │ │ │ │ │ $variables$plotDensity.list │ │ │ │ │ -[1] 112549 5316 │ │ │ │ │ +[1] 112557 5316 │ │ │ │ │ │ │ │ │ │ $variables$plotDensity.matrix │ │ │ │ │ -[1] 117865 461 │ │ │ │ │ +[1] 117873 461 │ │ │ │ │ │ │ │ │ │ $variables$plotDensity.numeric │ │ │ │ │ -[1] 118326 452 │ │ │ │ │ +[1] 118334 452 │ │ │ │ │ │ │ │ │ │ $variables$plotMvsA │ │ │ │ │ -[1] 118778 193 │ │ │ │ │ +[1] 118786 193 │ │ │ │ │ │ │ │ │ │ $variables$plotMvsA.matrix │ │ │ │ │ -[1] 118971 1233 │ │ │ │ │ +[1] 118979 1233 │ │ │ │ │ │ │ │ │ │ $variables$plotMvsAPairs │ │ │ │ │ -[1] 120204 197 │ │ │ │ │ +[1] 120212 197 │ │ │ │ │ │ │ │ │ │ $variables$plotMvsAPairs.matrix │ │ │ │ │ -[1] 120401 1516 │ │ │ │ │ +[1] 120409 1516 │ │ │ │ │ │ │ │ │ │ $variables$plotMvsMPairs │ │ │ │ │ -[1] 121917 197 │ │ │ │ │ +[1] 121925 197 │ │ │ │ │ │ │ │ │ │ $variables$plotMvsMPairs.matrix │ │ │ │ │ -[1] 122114 1435 │ │ │ │ │ +[1] 122122 1435 │ │ │ │ │ │ │ │ │ │ $variables$plotXYCurve │ │ │ │ │ -[1] 123549 196 │ │ │ │ │ +[1] 123557 196 │ │ │ │ │ │ │ │ │ │ $variables$plotXYCurve.matrix │ │ │ │ │ -[1] 123745 1678 │ │ │ │ │ +[1] 123753 1678 │ │ │ │ │ │ │ │ │ │ $variables$plotXYCurve.numeric │ │ │ │ │ -[1] 125423 4433 │ │ │ │ │ +[1] 125431 4433 │ │ │ │ │ │ │ │ │ │ $variables$predict.lowess │ │ │ │ │ -[1] 129856 380 │ │ │ │ │ +[1] 129864 380 │ │ │ │ │ │ │ │ │ │ $variables$print.SmoothSplineLikelihood │ │ │ │ │ -[1] 130236 1234 │ │ │ │ │ +[1] 130244 1234 │ │ │ │ │ │ │ │ │ │ $variables$projectUontoV │ │ │ │ │ -[1] 131470 627 │ │ │ │ │ +[1] 131478 627 │ │ │ │ │ │ │ │ │ │ $variables$robustSmoothSpline │ │ │ │ │ -[1] 132097 201 │ │ │ │ │ +[1] 132105 201 │ │ │ │ │ │ │ │ │ │ $variables$robustSmoothSpline.default │ │ │ │ │ -[1] 132298 4766 │ │ │ │ │ +[1] 132306 4766 │ │ │ │ │ │ │ │ │ │ $variables$rowAverages │ │ │ │ │ -[1] 137064 195 │ │ │ │ │ +[1] 137072 195 │ │ │ │ │ │ │ │ │ │ $variables$rowAverages.matrix │ │ │ │ │ -[1] 137259 2009 │ │ │ │ │ +[1] 137267 2009 │ │ │ │ │ │ │ │ │ │ $variables$sampleCorrelations │ │ │ │ │ -[1] 139268 198 │ │ │ │ │ +[1] 139276 198 │ │ │ │ │ │ │ │ │ │ $variables$sampleCorrelations.matrix │ │ │ │ │ -[1] 139466 2376 │ │ │ │ │ +[1] 139474 2376 │ │ │ │ │ │ │ │ │ │ $variables$sampleTuples │ │ │ │ │ -[1] 141842 194 │ │ │ │ │ +[1] 141850 194 │ │ │ │ │ │ │ │ │ │ $variables$sampleTuples.default │ │ │ │ │ -[1] 142036 1144 │ │ │ │ │ +[1] 142044 1144 │ │ │ │ │ │ │ │ │ │ $variables$scalarProduct │ │ │ │ │ -[1] 143180 297 │ │ │ │ │ +[1] 143188 297 │ │ │ │ │ │ │ │ │ │ $variables$tr │ │ │ │ │ -[1] 143477 277 │ │ │ │ │ +[1] 143485 277 │ │ │ │ │ │ │ │ │ │ $variables$wpca │ │ │ │ │ -[1] 143754 189 │ │ │ │ │ +[1] 143762 189 │ │ │ │ │ │ │ │ │ │ $variables$wpca.matrix │ │ │ │ │ -[1] 143943 4317 │ │ │ │ │ +[1] 143951 4317 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 293 821 │ │ │ │ │ +[1] 293 829 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 0 131 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 131 162 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 1166 131 │ │ │ │ │ +[1] 1174 131 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/aroma.light/help/aroma.light.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -197,15 +197,15 @@ │ │ │ │ structure(" by other means, it is possible to normalize the data robustly by\n", Rd_tag = "TEXT"), │ │ │ │ structure(" fitting the above affine model without intercept, that is, fitting\n", Rd_tag = "TEXT"), │ │ │ │ structure(" a truly linear model. This is done adding argument ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("center=FALSE", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" when calling ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("normalizeAffine()", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT"))), Rd_tag = "\\section"), │ │ │ │ - structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/1._Calibration_and_Normalization.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/1._Calibration_and_Normalization.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ Non-documented_objects (list) = structure(list(structure(list(structure("Non-documented objects", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("Non-documented objects", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("Non-documented objects", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("lines.XYCurveFit", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("rowAverages", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -225,15 +225,15 @@ │ │ │ │ structure(" functions that have specific\n", Rd_tag = "TEXT"), │ │ │ │ structure(" document for the corresponding method coupled to a specific class.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" Other functions are re-defined by ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("setMethodS3()", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(" to\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("default", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(" methods. Neither of these two classes are non-documented\n", Rd_tag = "TEXT"), │ │ │ │ - structure(" in reality.\n", Rd_tag = "TEXT"), structure(" The rest are deprecated methods.\n", Rd_tag = "TEXT")), Rd_tag = "\\description")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/Non-documented_objects.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" in reality.\n", Rd_tag = "TEXT"), structure(" The rest are deprecated methods.\n", Rd_tag = "TEXT")), Rd_tag = "\\description")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/Non-documented_objects.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ aroma.light-package (list) = structure(list(structure(list(structure("Package aroma.light", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("aroma.light-package", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("aroma.light-package", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("aroma.light", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("package", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -372,15 +372,15 @@ │ │ │ │ structure(", Bioinformatics, 2009.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(), Rd_tag = "\\cr"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("[8] H. Bengtsson, P. Neuvial and T.P. Speed, ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays", Rd_tag = "TEXT")), Rd_tag = "\\emph"), │ │ │ │ structure(", BMC Bioinformatics, 2010, 11:245. [PMID 20462408]\n", Rd_tag = "TEXT"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(), Rd_tag = "\\cr"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/aroma.light-package.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/aroma.light-package.Rd", class = "Rd", meta = list( │ │ │ │ docType = "package", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ averageQuantile (list) = structure(list(structure(list(structure("Gets the average empirical distribution", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("averageQuantile", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("averageQuantile", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("averageQuantile.list", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("averageQuantile.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -434,15 +434,15 @@ │ │ │ │ structure(" University of California.\n", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("normalizeQuantileRank", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("().\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("normalizeQuantileSpline", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("().\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("quantile", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("stats", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ - structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/averageQuantile.Rd", class = "Rd", meta = list( │ │ │ │ + structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/averageQuantile.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ backtransformAffine (list) = structure(list(structure(list(structure("Reverse affine transformation", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("backtransformAffine", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("backtransformAffine", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("backtransformAffine.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -561,15 +561,15 @@ │ │ │ │ structure("# If the columns of X are identical, and a identity\n", Rd_tag = "RCODE"), │ │ │ │ structure("# backtransformation is applied and projected, the\n", Rd_tag = "RCODE"), │ │ │ │ structure("# same matrix is returned.\n", Rd_tag = "RCODE"), │ │ │ │ structure("X <- matrix(1:4, nrow=4, ncol=3)\n", Rd_tag = "RCODE"), │ │ │ │ structure("X[,2] <- X[,2]*2; X[,3] <- X[,3]*3\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(X)\n", Rd_tag = "RCODE"), structure("Y <- backtransformAffine(X, b=c(1,2,3))\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(Y)\n", Rd_tag = "RCODE"), structure("Y <- backtransformAffine(X, b=c(1,2,3), project=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("print(Y)\n", Rd_tag = "RCODE"), structure("stopifnot(sum(X[,1]-Y) <= .Machine$double.eps)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/backtransformAffine.Rd", class = "Rd", meta = list( │ │ │ │ + structure("print(Y)\n", Rd_tag = "RCODE"), structure("stopifnot(sum(X[,1]-Y) <= .Machine$double.eps)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/backtransformAffine.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ backtransformPrincipalCurve (list) = structure(list(structure(list(structure("Reverse transformation of principal-curve fit", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("backtransformPrincipalCurve", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("backtransformPrincipalCurve", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("backtransformPrincipalCurve.numeric", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("backtransformPrincipalCurve.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -732,15 +732,15 @@ │ │ │ │ structure("# the the model fit of measurement #3 (because we believe these\n", Rd_tag = "RCODE"), │ │ │ │ structure("# two have undergone very similar transformations.\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Signals are standardized to target dimension 1.\n", Rd_tag = "RCODE"), │ │ │ │ structure("y7 <- Y[,2,drop=FALSE]\n", Rd_tag = "RCODE"), │ │ │ │ structure("yN7 <- backtransformPrincipalCurve(y7, fit=fit, dimensions=3,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" targetDimension=1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("stopifnot(ncol(yN7) == 1)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("stopifnot(cor(yN7, yN6) > 0.9999)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/backtransformPrincipalCurve.Rd", class = "Rd", meta = list( │ │ │ │ + structure("stopifnot(cor(yN7, yN6) > 0.9999)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/backtransformPrincipalCurve.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ calibrateMultiscan (list) = structure(list(structure(list(structure("Weighted affine calibration of a multiple re-scanned channel", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calibrateMultiscan", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calibrateMultiscan", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("calibrateMultiscan.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -934,15 +934,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(), Rd_tag = "\\cr"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("1. Calibration and Normalization", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("normalizeAffine", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("().\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ - structure(list(structure(list(structure("# For an example, see help(normalizeAffine).", Rd_tag = "VERB")), Rd_tag = "\\dontrun")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/calibrateMultiscan.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure(list(structure("# For an example, see help(normalizeAffine).", Rd_tag = "VERB")), Rd_tag = "\\dontrun")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/calibrateMultiscan.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ callNaiveGenotypes (list) = structure(list(structure(list(structure("Calls genotypes in a normal sample", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("callNaiveGenotypes", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("callNaiveGenotypes", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("callNaiveGenotypes.numeric", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -1053,15 +1053,15 @@ │ │ │ │ structure("x <- c(xAA,xAB,xBB)\n", Rd_tag = "RCODE"), │ │ │ │ structure("fit <- findPeaksAndValleys(x)\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(fit)\n", Rd_tag = "RCODE"), structure("calls <- callNaiveGenotypes(x)\n", Rd_tag = "RCODE"), │ │ │ │ structure("xc <- split(x, calls)\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(table(calls))\n", Rd_tag = "RCODE"), │ │ │ │ structure("xx <- c(list(x),xc)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotDensity(xx, adjust=1.5, lwd=2, col=seq_along(xx), main=\"(AA',AB',BB')\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("abline(v=fit$x)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/callNaiveGenotypes.Rd", class = "Rd", meta = list( │ │ │ │ + structure("abline(v=fit$x)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/callNaiveGenotypes.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ distanceBetweenLines (list) = structure(list(structure(list(structure("Finds the shortest distance between two lines", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("distanceBetweenLines", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("distanceBetweenLines.default", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("distanceBetweenLines", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("algebra", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -1219,15 +1219,15 @@ │ │ │ │ structure(" points3d(t(fit$yt), cex=1.5, col=\"blue\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" text3d(t(fit$yt), label=expression(y(t)), adj=c(-1,0.5))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" # Draw the distance between the two points\n", Rd_tag = "RCODE"), │ │ │ │ structure(" lines3d(rbind(fit$xs,fit$yt), col=\"purple\", lwd=2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(fit)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("} # for (zzz in 0)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("rm(zzz)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/distanceBetweenLines.Rd", class = "Rd", meta = list( │ │ │ │ + structure("rm(zzz)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/distanceBetweenLines.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ findPeaksAndValleys (list) = structure(list(structure(list(structure("Finds extreme points in the empirical density estimated from data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("findPeaksAndValleys", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("findPeaksAndValleys", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("findPeaksAndValleys.density", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("findPeaksAndValleys.numeric", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1305,15 +1305,15 @@ │ │ │ │ structure("x1b <- rnorm(n=10000, mean=0, sd=0.1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("x2b <- rnorm(n=10000, mean=4, sd=0.1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("x3b <- rnorm(n=10000, mean=8, sd=0.1)\n", Rd_tag = "RCODE"), │ │ │ │ structure("x <- c(x1b,x2b,x3b)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Illustrating explicit usage of density()\n", Rd_tag = "RCODE"), │ │ │ │ structure("d <- density(x)\n", Rd_tag = "RCODE"), structure("fit <- findPeaksAndValleys(d, tol=0)\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(fit)\n", Rd_tag = "RCODE"), structure("plot(d, lwd=2, main=\"c(x1b,x2b,x3b)\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("abline(v=fit$x)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/findPeaksAndValleys.Rd", class = "Rd", meta = list( │ │ │ │ + structure("abline(v=fit$x)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/findPeaksAndValleys.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ fitIWPCA (list) = structure(list(structure(list(structure("Robust fit of linear subspace through multidimensional data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitIWPCA", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitIWPCA", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("fitIWPCA.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -1518,15 +1518,15 @@ │ │ │ │ structure("()\n", Rd_tag = "TEXT"), structure(" and ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("normalizeAffine", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("() methods.\n", Rd_tag = "TEXT"), structure(" Internally the function ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("iwpca", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("() is used to fit a line\n", Rd_tag = "TEXT"), │ │ │ │ structure(" through the data cloud and the function ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("distanceBetweenLines", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("() to\n", Rd_tag = "TEXT"), structure(" find the closest point to the diagonal (1,1,...,1).\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/fitIWPCA.Rd", class = "Rd", meta = list( │ │ │ │ + structure("() to\n", Rd_tag = "TEXT"), structure(" find the closest point to the diagonal (1,1,...,1).\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/fitIWPCA.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ fitNaiveGenotypes (list) = structure(list(structure(list(structure("Fit naive genotype model from a normal sample", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitNaiveGenotypes", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitNaiveGenotypes", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("fitNaiveGenotypes.numeric", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -1612,15 +1612,15 @@ │ │ │ │ structure("list", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("base", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure("s.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" To call genotypes see ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("callNaiveGenotypes", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("().\n", Rd_tag = "TEXT"), structure(" Internally ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("findPeaksAndValleys", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ - structure("() is used to identify the thresholds.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/fitNaiveGenotypes.Rd", class = "Rd", meta = list( │ │ │ │ + structure("() is used to identify the thresholds.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/fitNaiveGenotypes.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ fitPrincipalCurve (list) = structure(list(structure(list(structure("Fit a principal curve in K dimensions", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitPrincipalCurve", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitPrincipalCurve", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("fitPrincipalCurve.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -1722,15 +1722,15 @@ │ │ │ │ structure(" plot(NA, xlim=ylim, ylim=ylim, xlab=xlab, ylab=ylab)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" abline(a=0, b=1, lty=2)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" points(y[,c(cc,rr)])\n", Rd_tag = "RCODE"), │ │ │ │ structure(" points(yN[,c(cc,rr)], col=\"tomato\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" legend(\"topleft\", col=c(\"black\", \"tomato\"), pch=19,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" c(\"orignal\", \"transformed\"), bty=\"n\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(" }\n", Rd_tag = "RCODE"), structure("}\n", Rd_tag = "RCODE"), │ │ │ │ - structure("title(main=\"Pairwise signals before and after transform\", outer=TRUE, line=-2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/fitPrincipalCurve.Rd", class = "Rd", meta = list( │ │ │ │ + structure("title(main=\"Pairwise signals before and after transform\", outer=TRUE, line=-2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/fitPrincipalCurve.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ fitXYCurve (list) = structure(list(structure(list(structure("Fitting a smooth curve through paired (x,y) data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fitXYCurve", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fitXYCurve", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("fitXYCurve.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("backtransformXYCurve", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -1859,15 +1859,15 @@ │ │ │ │ structure("subset <- sample(nrow(Y), size=0.3*nrow(Y))\n", Rd_tag = "RCODE"), │ │ │ │ structure("fit <- fitXYCurve(Y[subset,], bandwidth=0.2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("lines(fit, col=\"red\", lwd=2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Backtransform (y_1, y_2) keeping y_1 unchanged\n", Rd_tag = "RCODE"), │ │ │ │ structure("YN <- backtransformXYCurve(Y, fit=fit)\n", Rd_tag = "RCODE"), │ │ │ │ structure("points(YN, col=\"blue\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("abline(a=0, b=1, col=\"red\", lwd=2)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/fitXYCurve.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/fitXYCurve.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ iwpca (list) = structure(list(structure(list(structure("Fits an R-dimensional hyperplane using iterative re-weighted PCA", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("iwpca", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("iwpca", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -2021,15 +2021,15 @@ │ │ │ │ structure(" lines3d(t(yline), col=col[ii])\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" # Highlight the last one\n", Rd_tag = "RCODE"), │ │ │ │ structure(" if (ii == length(maxIter))\n", Rd_tag = "RCODE"), │ │ │ │ structure(" lines3d(t(yline), col=\"red\", lwd=3)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" }\n", Rd_tag = "RCODE"), structure("}\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("par(opar)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("} # for (zzz in 0)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("rm(zzz)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/iwpca.Rd", class = "Rd", meta = list( │ │ │ │ + structure("rm(zzz)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/iwpca.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ likelihood.smooth.spline (list) = structure(list(structure(list(structure("Calculate the log likelihood of a smoothing spline given the data", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("likelihood.smooth.spline", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("likelihood.smooth.spline", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("smooth", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -2186,15 +2186,15 @@ │ │ │ │ structure("print(l)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("# In cases with non unique x values one has to proceed as\n", Rd_tag = "RCODE"), │ │ │ │ structure("# below if one want to get the log likelihood for the original\n", Rd_tag = "RCODE"), │ │ │ │ structure("# data.\n", Rd_tag = "RCODE"), structure("l <- likelihood(g, x=x, y=y)\n", Rd_tag = "RCODE"), │ │ │ │ structure("cat(\"\\nLog likelihood of the *original* data set:\\n\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(l)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/likelihood.smooth.spline.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/likelihood.smooth.spline.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ medianPolish (list) = structure(list(structure(list(structure("Median polish", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("medianPolish", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("medianPolish", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("medianPolish.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -2287,15 +2287,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("print(deaths)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("mp <- medianPolish(deaths)\n", Rd_tag = "RCODE"), │ │ │ │ structure("mp1 <- medpolish(deaths, trace=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(mp)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("ff <- c(\"overall\", \"row\", \"col\", \"residuals\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("stopifnot(all.equal(mp[ff], mp1[ff]))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Validate decomposition:\n", Rd_tag = "RCODE"), │ │ │ │ - structure("stopifnot(all.equal(deaths, mp$overall+outer(mp$row,mp$col,\"+\")+mp$resid))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/medianPolish.Rd", class = "Rd", meta = list( │ │ │ │ + structure("stopifnot(all.equal(deaths, mp$overall+outer(mp$row,mp$col,\"+\")+mp$resid))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/medianPolish.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ normalizeAffine (list) = structure(list(structure(list(structure("Weighted affine normalization between channels and arrays", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("normalizeAffine", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("normalizeAffine", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("normalizeAffine.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -2550,15 +2550,15 @@ │ │ │ │ structure("plotMvsMPairs(cbind(rgCANa, rgCANlw), col=\"orange\", xlab=expression(M[affine]))\n", Rd_tag = "RCODE"), │ │ │ │ structure("title(main=\"Normalized AC\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotMvsMPairs(cbind(rgCANa, rgCANl), col=\"red\", add=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotMvsMPairs(cbind(rgCANa, rgCANrs), col=\"blue\", add=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("abline(a=0, b=1, lty=2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("legend(x=-6,y=6, legend=c(\"lowess\", \"loess\", \"r. spline\"), pch=19,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" col=c(\"orange\", \"red\", \"blue\"), ncol=2, x.intersp=0.3, bty=\"n\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeAffine.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/normalizeAffine.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ normalizeAverage (list) = structure(list(structure(list(structure("Rescales channel vectors to get the same average", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("normalizeAverage", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("normalizeAverage", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("normalizeAverage.list", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("normalizeAverage.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -2608,15 +2608,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Returns a normalized ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("numeric", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("base", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(" NxK ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("matrix", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("base", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(" (or ", Rd_tag = "TEXT"), structure(list(structure(list( │ │ │ │ structure("list", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("base", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(" of length K).\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeAverage.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/normalizeAverage.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ normalizeCurveFit (list) = structure(list(structure(list(structure("Weighted curve-fit normalization between a pair of channels", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("normalizeCurveFit", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("normalizeCurveFit", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("normalizeLoess", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("normalizeLowess", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -2883,15 +2883,15 @@ │ │ │ │ structure("plotMvsMPairs(cbind(rgCANa, rgCANlw), col=\"orange\", xlab=expression(M[affine]))\n", Rd_tag = "RCODE"), │ │ │ │ structure("title(main=\"Normalized AC\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotMvsMPairs(cbind(rgCANa, rgCANl), col=\"red\", add=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotMvsMPairs(cbind(rgCANa, rgCANrs), col=\"blue\", add=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("abline(a=0, b=1, lty=2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("legend(x=-6,y=6, legend=c(\"lowess\", \"loess\", \"r. spline\"), pch=19,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" col=c(\"orange\", \"red\", \"blue\"), ncol=2, x.intersp=0.3, bty=\"n\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeCurveFit.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/normalizeCurveFit.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ normalizeDifferencesToAverage (list) = structure(list(structure(list(structure("Rescales channel vectors to get the same average", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("normalizeDifferencesToAverage", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("normalizeDifferencesToAverage", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("normalizeDifferencesToAverage.list", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -2952,15 +2952,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Get the estimated parameters\n", Rd_tag = "RCODE"), │ │ │ │ structure("fit <- attr(yyN, \"fit\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Plot the tracks\n", Rd_tag = "RCODE"), │ │ │ │ structure("layout(matrix(1:2, ncol=1))\n", Rd_tag = "RCODE"), │ │ │ │ structure("x <- unlist(xx)\n", Rd_tag = "RCODE"), structure("col <- unlist(zz)\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- unlist(yy)\n", Rd_tag = "RCODE"), structure("yN <- unlist(yyN)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot(x, y, col=col, ylim=c(-10,10))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot(x, yN, col=col, ylim=c(-10,10))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeDifferencesToAverage.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot(x, yN, col=col, ylim=c(-10,10))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/normalizeDifferencesToAverage.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ normalizeFragmentLength (list) = structure(list(structure(list(structure("Normalizes signals for PCR fragment-length effects", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("normalizeFragmentLength", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("normalizeFragmentLength.default", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("normalizeFragmentLength", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("nonparametric", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -3271,15 +3271,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" uu <- unitSets$none\n", Rd_tag = "RCODE"), │ │ │ │ structure(" if (length(uu) > 0)\n", Rd_tag = "RCODE"), │ │ │ │ structure(" data[[4]] <- M[uu,ii]\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" cols <- seq_along(data)+1\n", Rd_tag = "RCODE"), │ │ │ │ structure(" plotDensity(data, col=cols, xlim=Mlim, xlab=Mlab, main=\"normalized\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure(" abline(v=0, lty=2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("}\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeFragmentLength.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/normalizeFragmentLength.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ normalizeQuantileRank (list) = structure(list(structure(list(structure("Normalizes the empirical distribution of one of more samples to a target distribution", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("normalizeQuantileRank", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("normalizeQuantileRank", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("normalizeQuantileRank.numeric", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("normalizeQuantileRank.list", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -3395,15 +3395,15 @@ │ │ │ │ structure(" x\n", Rd_tag = "RCODE"), structure("})\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Normalize quantiles\n", Rd_tag = "RCODE"), │ │ │ │ structure("Xn <- normalizeQuantile(X)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Plot the data\n", Rd_tag = "RCODE"), │ │ │ │ structure("layout(matrix(1:2, ncol=1))\n", Rd_tag = "RCODE"), │ │ │ │ structure("xlim <- range(X, na.rm=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotDensity(X, lwd=2, xlim=xlim, main=\"The original distributions\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plotDensity(Xn, lwd=2, xlim=xlim, main=\"The normalized distributions\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeQuantileRank.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plotDensity(Xn, lwd=2, xlim=xlim, main=\"The normalized distributions\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/normalizeQuantileRank.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ normalizeQuantileRank.matrix (list) = structure(list(structure(list(structure("Normalizes the empirical distribution of a set of samples to a common target distribution", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("normalizeQuantileRank.matrix", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("normalizeQuantileRank.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ structure(list(structure("nonparametric", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -3504,15 +3504,15 @@ │ │ │ │ structure("X[sample(3*N, size=0.20*3*N)] <- NA\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Normalize quantiles\n", Rd_tag = "RCODE"), │ │ │ │ structure("Xn <- normalizeQuantile(X)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Plot the data\n", Rd_tag = "RCODE"), │ │ │ │ structure("layout(matrix(1:2, ncol=1))\n", Rd_tag = "RCODE"), │ │ │ │ structure("xlim <- range(X, Xn, na.rm=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotDensity(X, lwd=2, xlim=xlim, main=\"The three original distributions\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plotDensity(Xn, lwd=2, xlim=xlim, main=\"The three normalized distributions\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeQuantileRank.matrix.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plotDensity(Xn, lwd=2, xlim=xlim, main=\"The three normalized distributions\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/normalizeQuantileRank.matrix.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ normalizeQuantileSpline (list) = structure(list(structure(list(structure("Normalizes the empirical distribution of one or more samples to a target distribution", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("normalizeQuantileSpline", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("normalizeQuantileSpline", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("normalizeQuantileSpline.numeric", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("normalizeQuantileSpline.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -3659,15 +3659,15 @@ │ │ │ │ structure("xlim <- range(X, na.rm=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotDensity(X, lwd=2, xlim=xlim, main=\"The three original distributions\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("Xn <- normalizeQuantile(X)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotDensity(Xn, lwd=2, xlim=xlim, main=\"The three normalized distributions\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotXYCurve(X, Xn, xlim=xlim, main=\"The three normalized distributions\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("Xn2 <- normalizeQuantileSpline(X, xTarget=Xn[,1], spar=0.99)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plotDensity(Xn2, lwd=2, xlim=xlim, main=\"The three normalized distributions\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plotXYCurve(X, Xn2, xlim=xlim, main=\"The three normalized distributions\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeQuantileSpline.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plotXYCurve(X, Xn2, xlim=xlim, main=\"The three normalized distributions\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/normalizeQuantileSpline.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ normalizeTumorBoost (list) = structure(list(structure(list(structure("Normalizes allele B fractions for a tumor given a match normal", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("normalizeTumorBoost", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("normalizeTumorBoost", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("normalizeTumorBoost.numeric", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -3825,15 +3825,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Allele B fractions for the tumor sample\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot(pos, betaT, col=col, ylim=ylim)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# TumorBoost w/ naive genotype calls\n", Rd_tag = "RCODE"), │ │ │ │ structure("betaTN <- normalizeTumorBoost(betaT=betaT, betaN=betaN, preserveScale=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot(pos, betaTN, col=col, ylim=ylim)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# TumorBoost w/ external multi-sample genotype calls\n", Rd_tag = "RCODE"), │ │ │ │ structure("betaTNx <- normalizeTumorBoost(betaT=betaT, betaN=betaN, muN=muN, preserveScale=FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot(pos, betaTNx, col=col, ylim=ylim)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeTumorBoost.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot(pos, betaTNx, col=col, ylim=ylim)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/normalizeTumorBoost.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ pairedAlleleSpecificCopyNumbers (list) = structure(list(structure(list(structure("Calculating tumor-normal paired allele-specific copy number stratified on genotypes", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("pairedAlleleSpecificCopyNumbers", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("pairedAlleleSpecificCopyNumbers", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("pairedAlleleSpecificCopyNumbers.numeric", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -3872,15 +3872,15 @@ │ │ │ │ structure(" and ", Rd_tag = "TEXT"), structure(list(structure("muN", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(".\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("Pierre Neuvial, Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" This definition of calculating tumor-normal paired ASCN is related\n", Rd_tag = "TEXT"), │ │ │ │ structure(" to how the ", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure(list(structure("normalizeTumorBoost", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("() method calculates normalized\n", Rd_tag = "TEXT"), │ │ │ │ - structure(" tumor BAFs.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/pairedAlleleSpecificCopyNumbers.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" tumor BAFs.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/pairedAlleleSpecificCopyNumbers.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotDensity (list) = structure(list(structure(list(structure("Plots density distributions for a set of vectors", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotDensity", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotDensity", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("plotDensity.list", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("plotDensity.data.frame", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -3964,15 +3964,15 @@ │ │ │ │ structure(", the curves are plotted in the current plot,\n", Rd_tag = "TEXT"), │ │ │ │ structure(" otherwise a new is created.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Internally, ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure(list(structure("density", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("stats", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(" is used to estimate the\n", Rd_tag = "TEXT"), │ │ │ │ - structure(" empirical density.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/plotDensity.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" empirical density.\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/plotDensity.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotMvsA (list) = structure(list(structure(list(structure("Plot log-ratios vs log-intensities", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotMvsA", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotMvsA", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("plotMvsA.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -4013,15 +4013,15 @@ │ │ │ │ structure(list(structure("TRUE", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("base:logical", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(", data points are plotted in the current plot,\n", Rd_tag = "TEXT"), │ │ │ │ structure(" otherwise a new plot is created.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Red channel is assumed to be in column one and green in column two.\n", Rd_tag = "TEXT"), │ │ │ │ structure(" Log-ratio are calculated taking channel one over channel two.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Returns nothing.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/plotMvsA.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/plotMvsA.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotMvsAPairs (list) = structure(list(structure(list(structure("Plot log-ratios/log-intensities for all unique pairs of data vectors", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotMvsAPairs", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotMvsAPairs", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("plotMvsAPairs.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -4060,15 +4060,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Log-ratios and log-intensities are calculated for each neighboring pair\n", Rd_tag = "TEXT"), │ │ │ │ structure(" of channels (columns) and plotted. Thus, in total there will be K-1\n", Rd_tag = "TEXT"), │ │ │ │ structure(" data set plotted.\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(" The colors used for the plotted pairs are 1, 2, and so on. To change\n", Rd_tag = "TEXT"), │ │ │ │ structure(" the colors, use a different color palette.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Returns nothing.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/plotMvsAPairs.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/plotMvsAPairs.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotMvsMPairs (list) = structure(list(structure(list(structure("Plot log-ratios vs log-ratios for all pairs of columns", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotMvsMPairs", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotMvsMPairs", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("plotMvsMPairs.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -4104,15 +4104,15 @@ │ │ │ │ structure(list(structure("TRUE", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("base:logical", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(", data points are plotted in the current plot,\n", Rd_tag = "TEXT"), │ │ │ │ structure(" otherwise a new plot is created.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Log-ratio are calculated by over paired columns, e.g. column 1 and 2,\n", Rd_tag = "TEXT"), │ │ │ │ structure(" column 3 and 4, and so on.\n", Rd_tag = "TEXT")), Rd_tag = "\\details"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Returns nothing.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/plotMvsMPairs.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/plotMvsMPairs.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ plotXYCurve (list) = structure(list(structure(list(structure("Plot the relationship between two variables as a smooth curve", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plotXYCurve", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plotXYCurve", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("plotXYCurve.numeric", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("plotXYCurve.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -4195,15 +4195,15 @@ │ │ │ │ structure(list(structure("TRUE", Rd_tag = "TEXT")), Rd_tag = "\\link", Rd_option = structure("base:logical", Rd_tag = "TEXT"))), Rd_tag = "\\code"), │ │ │ │ structure(", the graph is added to the current plot, otherwise\n", Rd_tag = "TEXT"), │ │ │ │ structure(" a new plot is created.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Returns nothing.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(list(structure("Missing values", Rd_tag = "TEXT")), │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure(" Data points (x,y) with non-finite values are excluded.\n", Rd_tag = "TEXT"))), Rd_tag = "\\section"), │ │ │ │ - structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/plotXYCurve.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/plotXYCurve.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ print.SmoothSplineLikelihood (list) = structure(list(structure(list(structure("Prints an SmoothSplineLikelihood object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("print.SmoothSplineLikelihood", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("print.SmoothSplineLikelihood", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("SmoothSplineLikelihood.print", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("print,SmoothSplineLikelihood-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -4224,15 +4224,15 @@ │ │ │ │ structure(list(list(structure("digits", Rd_tag = "TEXT")), │ │ │ │ list(structure("Minimal number of significant digits to print.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("...", Rd_tag = "TEXT")), │ │ │ │ list(structure("Not used.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(" Returns nothing.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ - structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/print.SmoothSplineLikelihood.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("Henrik Bengtsson", Rd_tag = "TEXT")), Rd_tag = "\\author")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/print.SmoothSplineLikelihood.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ robustSmoothSpline (list) = structure(list(structure(list(structure("Robust fit of a Smoothing Spline", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("robustSmoothSpline", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("robustSmoothSpline.default", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("robustSmoothSpline", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("smooth", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -4367,15 +4367,15 @@ │ │ │ │ structure("lines(smooth.spline(speed, dist, df=10), lty=2, col = \"blue\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Fit a smoothing spline using L_1 norm with 10 degrees of freedom\n", Rd_tag = "RCODE"), │ │ │ │ structure("lines(robustSmoothSpline(speed, dist, df=10), lty=2, col = \"red\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("legend(5,120, c(\n", Rd_tag = "RCODE"), │ │ │ │ structure(" paste(\"smooth.spline [C.V.] => df =\",round(cars.spl$df,1)),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" paste(\"robustSmoothSpline [C.V.] => df =\",round(cars.rspl$df,1)),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \"standard with s( * , df = 10)\", \"robust with s( * , df = 10)\"\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" ), col = c(\"blue\",\"red\",\"blue\",\"red\"), lty = c(1,1,2,2), bg='bisque')\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/robustSmoothSpline.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" ), col = c(\"blue\",\"red\",\"blue\",\"red\"), lty = c(1,1,2,2), bg='bisque')\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/robustSmoothSpline.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -4440,15 +4440,15 @@ │ │ │ │ structure("().\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Simulate 20000 genes with 10 observations each\n", Rd_tag = "RCODE"), │ │ │ │ structure("X <- matrix(rnorm(n=20000), ncol=10)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("# Calculate the correlation for 5000 random gene pairs\n", Rd_tag = "RCODE"), │ │ │ │ structure("cor <- sampleCorrelations(X, npairs=5000)\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(summary(cor))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/sampleCorrelations.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/sampleCorrelations.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ sampleTuples (list) = structure(list(structure(list(structure("Sample tuples of elements from a set", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("sampleTuples", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("sampleTuples.default", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("sampleTuples", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("utilities", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -4487,15 +4487,15 @@ │ │ │ │ structure("().\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("pairs <- sampleTuples(1:10, size=5, length=2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(pairs)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("triples <- sampleTuples(1:10, size=5, length=3)\n", Rd_tag = "RCODE"), │ │ │ │ structure("print(triples)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Allow tuples with repeated elements\n", Rd_tag = "RCODE"), │ │ │ │ structure("quadruples <- sampleTuples(1:3, size=5, length=4, replace=TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("print(quadruples)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/sampleTuples.Rd", class = "Rd", meta = list( │ │ │ │ + structure("print(quadruples)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/sampleTuples.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ wpca (list) = structure(list(structure(list(structure("Light-weight Weighted Principal Component Analysis", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("wpca", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("wpca", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("wpca.matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("methods", Rd_tag = "TEXT")), Rd_tag = "\\keyword"), │ │ │ │ @@ -4733,10 +4733,10 @@ │ │ │ │ structure("b <- fit$vt[1,2]/fit$vt[1,1]\n", Rd_tag = "RCODE"), │ │ │ │ structure("a <- fit$xMean[2]-b*fit$xMean[1]\n", Rd_tag = "RCODE"), │ │ │ │ structure("abline(a=a, b=b, lty=2, lwd=2, col=3)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("legend(xlim[1],ylim[2], legend=c(\"lm(y~x)\", \"lm(y~x-1)\", \"lm(x~y)\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \"lm(x~y-1)\", \"pca\", \"pca w/o intercept\"), lty=rep(1:2,3),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" lwd=rep(c(1,1,2),each=2), col=rep(1:3,each=2))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("palette(opalette)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("par(opar)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-aroma.light/man/wpca.Rd", class = "Rd", meta = list( │ │ │ │ + structure("par(opar)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/wpca.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/aroma.light/help/aroma.light.rdx │ │ │ ├── aroma.light.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,229 +1,229 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$`1._Calibration_and_Normalization` │ │ │ │ │ -[1] 300 7628 │ │ │ │ │ +[1] 309 7638 │ │ │ │ │ │ │ │ │ │ $variables$`Non-documented_objects` │ │ │ │ │ -[1] 8227 1316 │ │ │ │ │ +[1] 8256 1328 │ │ │ │ │ │ │ │ │ │ $variables$`aroma.light-package` │ │ │ │ │ -[1] 9826 5570 │ │ │ │ │ +[1] 9877 5580 │ │ │ │ │ │ │ │ │ │ $variables$averageQuantile │ │ │ │ │ -[1] 15690 2478 │ │ │ │ │ +[1] 15761 2490 │ │ │ │ │ │ │ │ │ │ $variables$backtransformAffine │ │ │ │ │ -[1] 18464 4032 │ │ │ │ │ +[1] 18558 4042 │ │ │ │ │ │ │ │ │ │ $variables$backtransformPrincipalCurve │ │ │ │ │ -[1] 22797 5562 │ │ │ │ │ +[1] 22913 5573 │ │ │ │ │ │ │ │ │ │ $variables$calibrateMultiscan │ │ │ │ │ -[1] 28647 7680 │ │ │ │ │ +[1] 28785 7690 │ │ │ │ │ │ │ │ │ │ $variables$callNaiveGenotypes │ │ │ │ │ -[1] 36624 3804 │ │ │ │ │ +[1] 36783 3816 │ │ │ │ │ │ │ │ │ │ $variables$distanceBetweenLines │ │ │ │ │ -[1] 40724 4982 │ │ │ │ │ +[1] 40907 4991 │ │ │ │ │ │ │ │ │ │ $variables$findPeaksAndValleys │ │ │ │ │ -[1] 46004 2986 │ │ │ │ │ +[1] 46207 2997 │ │ │ │ │ │ │ │ │ │ $variables$fitIWPCA │ │ │ │ │ -[1] 49280 7041 │ │ │ │ │ +[1] 49505 7053 │ │ │ │ │ │ │ │ │ │ $variables$fitNaiveGenotypes │ │ │ │ │ -[1] 56618 3448 │ │ │ │ │ +[1] 56866 3459 │ │ │ │ │ │ │ │ │ │ $variables$fitPrincipalCurve │ │ │ │ │ -[1] 60362 4235 │ │ │ │ │ +[1] 60632 4246 │ │ │ │ │ │ │ │ │ │ $variables$fitXYCurve │ │ │ │ │ -[1] 64888 4899 │ │ │ │ │ +[1] 65180 4911 │ │ │ │ │ │ │ │ │ │ $variables$iwpca │ │ │ │ │ -[1] 70073 5900 │ │ │ │ │ +[1] 70388 5911 │ │ │ │ │ │ │ │ │ │ $variables$likelihood.smooth.spline │ │ │ │ │ -[1] 76272 5633 │ │ │ │ │ +[1] 76609 5644 │ │ │ │ │ │ │ │ │ │ $variables$medianPolish │ │ │ │ │ -[1] 82196 3651 │ │ │ │ │ +[1] 82554 3661 │ │ │ │ │ │ │ │ │ │ $variables$normalizeAffine │ │ │ │ │ -[1] 86135 9567 │ │ │ │ │ +[1] 86512 9577 │ │ │ │ │ │ │ │ │ │ $variables$normalizeAverage │ │ │ │ │ -[1] 95998 2141 │ │ │ │ │ +[1] 96394 2152 │ │ │ │ │ │ │ │ │ │ $variables$normalizeCurveFit │ │ │ │ │ -[1] 98429 9247 │ │ │ │ │ +[1] 98846 9257 │ │ │ │ │ │ │ │ │ │ $variables$normalizeDifferencesToAverage │ │ │ │ │ -[1] 107980 2730 │ │ │ │ │ +[1] 108419 2741 │ │ │ │ │ │ │ │ │ │ $variables$normalizeFragmentLength │ │ │ │ │ -[1] 111010 9467 │ │ │ │ │ +[1] 111471 9477 │ │ │ │ │ │ │ │ │ │ $variables$normalizeQuantileRank │ │ │ │ │ -[1] 120776 4571 │ │ │ │ │ +[1] 121257 4581 │ │ │ │ │ │ │ │ │ │ $variables$normalizeQuantileRank.matrix │ │ │ │ │ -[1] 125650 4264 │ │ │ │ │ +[1] 126152 4275 │ │ │ │ │ │ │ │ │ │ $variables$normalizeQuantileSpline │ │ │ │ │ -[1] 130213 5425 │ │ │ │ │ +[1] 130737 5435 │ │ │ │ │ │ │ │ │ │ $variables$normalizeTumorBoost │ │ │ │ │ -[1] 135935 6005 │ │ │ │ │ +[1] 136480 6016 │ │ │ │ │ │ │ │ │ │ $variables$pairedAlleleSpecificCopyNumbers │ │ │ │ │ -[1] 142247 1962 │ │ │ │ │ +[1] 142813 1973 │ │ │ │ │ │ │ │ │ │ $variables$plotDensity │ │ │ │ │ -[1] 144500 3079 │ │ │ │ │ +[1] 145087 3088 │ │ │ │ │ │ │ │ │ │ $variables$plotMvsA │ │ │ │ │ -[1] 147869 1953 │ │ │ │ │ +[1] 148475 1964 │ │ │ │ │ │ │ │ │ │ $variables$plotMvsAPairs │ │ │ │ │ -[1] 150116 1971 │ │ │ │ │ +[1] 150743 1982 │ │ │ │ │ │ │ │ │ │ $variables$plotMvsMPairs │ │ │ │ │ -[1] 152381 1794 │ │ │ │ │ +[1] 153029 1804 │ │ │ │ │ │ │ │ │ │ $variables$plotXYCurve │ │ │ │ │ -[1] 154467 3156 │ │ │ │ │ +[1] 155135 3169 │ │ │ │ │ │ │ │ │ │ $variables$print.SmoothSplineLikelihood │ │ │ │ │ -[1] 157926 1248 │ │ │ │ │ +[1] 158618 1260 │ │ │ │ │ │ │ │ │ │ $variables$robustSmoothSpline │ │ │ │ │ -[1] 159469 4890 │ │ │ │ │ +[1] 160185 4900 │ │ │ │ │ │ │ │ │ │ $variables$sampleCorrelations │ │ │ │ │ -[1] 164653 2513 │ │ │ │ │ +[1] 165390 2526 │ │ │ │ │ │ │ │ │ │ $variables$sampleTuples │ │ │ │ │ -[1] 167458 1812 │ │ │ │ │ +[1] 168218 1823 │ │ │ │ │ │ │ │ │ │ $variables$wpca │ │ │ │ │ -[1] 169555 8567 │ │ │ │ │ +[1] 170338 8576 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 300 │ │ │ │ │ +[1] 0 309 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 45706 298 │ │ │ │ │ +[1] 45898 309 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 48990 290 │ │ │ │ │ +[1] 49204 301 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 56321 297 │ │ │ │ │ +[1] 56558 308 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 60066 296 │ │ │ │ │ +[1] 60325 307 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 64597 291 │ │ │ │ │ +[1] 64878 302 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 69787 286 │ │ │ │ │ +[1] 70091 297 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 75973 299 │ │ │ │ │ +[1] 76299 310 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 81905 291 │ │ │ │ │ +[1] 82253 301 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 85847 288 │ │ │ │ │ +[1] 86215 297 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 95702 296 │ │ │ │ │ +[1] 96089 305 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ -[1] 7928 299 │ │ │ │ │ +[1] 7947 309 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 98139 290 │ │ │ │ │ +[1] 98546 300 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 107676 304 │ │ │ │ │ +[1] 108103 316 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 110710 300 │ │ │ │ │ +[1] 111160 311 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 120477 299 │ │ │ │ │ +[1] 120948 309 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 125347 303 │ │ │ │ │ +[1] 125838 314 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 129914 299 │ │ │ │ │ +[1] 130427 310 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ -[1] 135638 297 │ │ │ │ │ +[1] 136172 308 │ │ │ │ │ │ │ │ │ │ $references$`env::27` │ │ │ │ │ -[1] 141940 307 │ │ │ │ │ +[1] 142496 317 │ │ │ │ │ │ │ │ │ │ $references$`env::28` │ │ │ │ │ -[1] 144209 291 │ │ │ │ │ +[1] 144786 301 │ │ │ │ │ │ │ │ │ │ $references$`env::29` │ │ │ │ │ -[1] 147579 290 │ │ │ │ │ +[1] 148175 300 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ -[1] 9543 283 │ │ │ │ │ +[1] 9584 293 │ │ │ │ │ │ │ │ │ │ $references$`env::30` │ │ │ │ │ -[1] 149822 294 │ │ │ │ │ +[1] 150439 304 │ │ │ │ │ │ │ │ │ │ $references$`env::31` │ │ │ │ │ -[1] 152087 294 │ │ │ │ │ +[1] 152725 304 │ │ │ │ │ │ │ │ │ │ $references$`env::32` │ │ │ │ │ -[1] 154175 292 │ │ │ │ │ +[1] 154833 302 │ │ │ │ │ │ │ │ │ │ $references$`env::33` │ │ │ │ │ -[1] 157623 303 │ │ │ │ │ +[1] 158304 314 │ │ │ │ │ │ │ │ │ │ $references$`env::34` │ │ │ │ │ -[1] 159174 295 │ │ │ │ │ +[1] 159878 307 │ │ │ │ │ │ │ │ │ │ $references$`env::35` │ │ │ │ │ -[1] 164359 294 │ │ │ │ │ +[1] 165085 305 │ │ │ │ │ │ │ │ │ │ $references$`env::36` │ │ │ │ │ -[1] 167166 292 │ │ │ │ │ +[1] 167916 302 │ │ │ │ │ │ │ │ │ │ $references$`env::37` │ │ │ │ │ -[1] 169270 285 │ │ │ │ │ +[1] 170041 297 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 15396 294 │ │ │ │ │ +[1] 15457 304 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 18168 296 │ │ │ │ │ +[1] 18251 307 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 22496 301 │ │ │ │ │ +[1] 22600 313 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 28359 288 │ │ │ │ │ +[1] 28486 299 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 36327 297 │ │ │ │ │ +[1] 36475 308 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 40428 296 │ │ │ │ │ +[1] 40599 308 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/aroma.light/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,39 +1,39 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-aroma.light/man/1._Calibration_and_Normalization.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-aroma.light/man/Non-documented_objects.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-aroma.light/man/aroma.light-package.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-aroma.light/man/averageQuantile.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-aroma.light/man/backtransformAffine.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-aroma.light/man/backtransformPrincipalCurve.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-aroma.light/man/calibrateMultiscan.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-aroma.light/man/callNaiveGenotypes.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-aroma.light/man/distanceBetweenLines.Rd" │ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-aroma.light/man/findPeaksAndValleys.Rd" │ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-aroma.light/man/fitIWPCA.Rd" │ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-aroma.light/man/fitNaiveGenotypes.Rd" │ │ │ │ │ -[13] "/home/moeller/Salsa/r-bioc-aroma.light/man/fitPrincipalCurve.Rd" │ │ │ │ │ -[14] "/home/moeller/Salsa/r-bioc-aroma.light/man/fitXYCurve.Rd" │ │ │ │ │ -[15] "/home/moeller/Salsa/r-bioc-aroma.light/man/iwpca.Rd" │ │ │ │ │ -[16] "/home/moeller/Salsa/r-bioc-aroma.light/man/likelihood.smooth.spline.Rd" │ │ │ │ │ -[17] "/home/moeller/Salsa/r-bioc-aroma.light/man/medianPolish.Rd" │ │ │ │ │ -[18] "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeAffine.Rd" │ │ │ │ │ -[19] "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeAverage.Rd" │ │ │ │ │ -[20] "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeCurveFit.Rd" │ │ │ │ │ -[21] "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeDifferencesToAverage.Rd" │ │ │ │ │ -[22] "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeFragmentLength.Rd" │ │ │ │ │ -[23] "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeQuantileRank.Rd" │ │ │ │ │ -[24] "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeQuantileRank.matrix.Rd" │ │ │ │ │ -[25] "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeQuantileSpline.Rd" │ │ │ │ │ -[26] "/home/moeller/Salsa/r-bioc-aroma.light/man/normalizeTumorBoost.Rd" │ │ │ │ │ -[27] "/home/moeller/Salsa/r-bioc-aroma.light/man/pairedAlleleSpecificCopyNumbers.Rd" │ │ │ │ │ -[28] "/home/moeller/Salsa/r-bioc-aroma.light/man/plotDensity.Rd" │ │ │ │ │ -[29] "/home/moeller/Salsa/r-bioc-aroma.light/man/plotMvsA.Rd" │ │ │ │ │ -[30] "/home/moeller/Salsa/r-bioc-aroma.light/man/plotMvsAPairs.Rd" │ │ │ │ │ -[31] "/home/moeller/Salsa/r-bioc-aroma.light/man/plotMvsMPairs.Rd" │ │ │ │ │ -[32] "/home/moeller/Salsa/r-bioc-aroma.light/man/plotXYCurve.Rd" │ │ │ │ │ -[33] "/home/moeller/Salsa/r-bioc-aroma.light/man/print.SmoothSplineLikelihood.Rd" │ │ │ │ │ -[34] "/home/moeller/Salsa/r-bioc-aroma.light/man/robustSmoothSpline.Rd" │ │ │ │ │ -[35] "/home/moeller/Salsa/r-bioc-aroma.light/man/sampleCorrelations.Rd" │ │ │ │ │ -[36] "/home/moeller/Salsa/r-bioc-aroma.light/man/sampleTuples.Rd" │ │ │ │ │ -[37] "/home/moeller/Salsa/r-bioc-aroma.light/man/wpca.Rd" │ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/1._Calibration_and_Normalization.Rd" │ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/Non-documented_objects.Rd" │ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-aroma.light-3.42.0/man/aroma.light-package.Rd" │ 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