--- /srv/rebuilderd/tmp/rebuilderdDnDQw6/inputs/r-bioc-mutationalpatterns_3.22.0+dfsg-1_all.deb +++ /srv/rebuilderd/tmp/rebuilderdDnDQw6/out/r-bioc-mutationalpatterns_3.22.0+dfsg-1_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2026-08-12 16:10:47.000000 debian-binary │ --rw-r--r-- 0 0 0 3820 2026-08-12 16:10:47.000000 control.tar.xz │ --rw-r--r-- 0 0 0 2491048 2026-08-12 16:10:47.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 3744 2026-08-12 16:10:47.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 2493036 2026-08-12 16:10:47.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:10:47.000000 ./ │ │ │ --rw-r--r-- 0 root (0) root (0) 1410 2026-08-12 16:10:47.000000 ./control │ │ │ --rw-r--r-- 0 root (0) root (0) 11034 2026-08-12 16:10:47.000000 ./md5sums │ │ │ +-rw-r--r-- 0 root (0) root (0) 1275 2026-08-12 16:10:47.000000 ./control │ │ │ +-rw-r--r-- 0 root (0) root (0) 10940 2026-08-12 16:10:47.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,14 +1,14 @@ │ │ │ Package: r-bioc-mutationalpatterns │ │ │ Version: 3.22.0+dfsg-1 │ │ │ Architecture: all │ │ │ Maintainer: Debian R Packages Maintainers │ │ │ -Installed-Size: 4613 │ │ │ +Installed-Size: 4614 │ │ │ Depends: r-api-4.0, r-api-bioc-3.23, r-bioc-genomicranges (>= 1.24.0), r-cran-nmf (>= 0.20.6), r-bioc-s4vectors, r-bioc-biocgenerics (>= 0.18.0), r-bioc-bsgenome (>= 1.40.0), r-bioc-variantannotation (>= 1.18.1), r-cran-dplyr (>= 0.8.3), r-cran-tibble (>= 2.1.3), r-cran-purrr (>= 0.3.2), r-cran-tidyr (>= 1.0.0), r-cran-stringr (>= 1.4.0), r-cran-magrittr (>= 1.5), r-cran-ggplot2 (>= 2.1.0), r-cran-pracma (>= 1.8.8), r-bioc-iranges (>= 2.6.0), r-bioc-seqinfo, r-bioc-genomeinfodb (>= 1.45.9), r-bioc-biostrings (>= 2.40.0), r-cran-ggdendro (>= 0.1-20), r-cran-cowplot (>= 0.9.2), r-cran-ggalluvial (>= 0.12.2), r-cran-rcolorbrewer, r-pkg-team-core-architecture │ │ │ -Suggests: r-bioc-biocstyle (>= 2.0.3), r-bioc-biomart (>= 2.28.0), r-cran-gridextra (>= 2.2.1), r-bioc-rtracklayer (>= 1.32.2), r-bioc-genomicfeatures, r-bioc-annotationdbi, r-cran-testthat, r-cran-knitr, r-cran-rmarkdown │ │ │ +Suggests: r-bioc-rtracklayer (>= 1.32.2), r-bioc-genomicfeatures, r-bioc-annotationdbi │ │ │ Section: gnu-r │ │ │ Priority: optional │ │ │ Homepage: https://bioconductor.org/packages/MutationalPatterns/ │ │ │ Description: GNU R comprehensive genome-wide analysis of mutational processes │ │ │ This BioConductor package provides an extensive toolset for the │ │ │ characterization and visualization of a wide range of mutational patterns │ │ │ in base substitution catalogs. │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ │ │ │ ├── line order │ │ │ │ @@ -3,15 +3,14 @@ │ │ │ │ usr/lib/R/site-library/MutationalPatterns/INDEX │ │ │ │ usr/lib/R/site-library/MutationalPatterns/Meta/Rd.rds │ │ │ │ usr/lib/R/site-library/MutationalPatterns/Meta/features.rds │ │ │ │ usr/lib/R/site-library/MutationalPatterns/Meta/hsearch.rds │ │ │ │ usr/lib/R/site-library/MutationalPatterns/Meta/links.rds │ │ │ │ usr/lib/R/site-library/MutationalPatterns/Meta/nsInfo.rds │ │ │ │ usr/lib/R/site-library/MutationalPatterns/Meta/package.rds │ │ │ │ -usr/lib/R/site-library/MutationalPatterns/Meta/vignette.rds │ │ │ │ usr/lib/R/site-library/MutationalPatterns/NAMESPACE │ │ │ │ usr/lib/R/site-library/MutationalPatterns/NEWS │ │ │ │ usr/lib/R/site-library/MutationalPatterns/R/MutationalPatterns │ │ │ │ usr/lib/R/site-library/MutationalPatterns/R/MutationalPatterns.rdb │ │ │ │ usr/lib/R/site-library/MutationalPatterns/R/MutationalPatterns.rdx │ │ │ │ usr/lib/R/site-library/MutationalPatterns/README.md │ │ │ │ usr/lib/R/site-library/MutationalPatterns/doc/Introduction_to_MutationalPatterns.R ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -10,26 +10,25 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/Meta/ │ │ │ -rw-r--r-- 0 root (0) root (0) 3171 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/Meta/Rd.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 123 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/Meta/features.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 2824 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/Meta/hsearch.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 1273 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/Meta/links.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 921 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/Meta/nsInfo.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 2716 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/Meta/package.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 223 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/Meta/vignette.rds │ │ │ -rw-r--r-- 0 root (0) root (0) 2253 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/NAMESPACE │ │ │ -rw-r--r-- 0 root (0) root (0) 22574 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/NEWS │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/R/ │ │ │ -rw-r--r-- 0 root (0) root (0) 1058 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/R/MutationalPatterns │ │ │ --rw-r--r-- 0 root (0) root (0) 505896 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/R/MutationalPatterns.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 505911 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/R/MutationalPatterns.rdb │ │ │ -rw-r--r-- 0 root (0) root (0) 3263 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/R/MutationalPatterns.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 1428 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/README.md │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/doc/ │ │ │ -rw-r--r-- 0 root (0) root (0) 29043 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/doc/Introduction_to_MutationalPatterns.R │ │ │ -rw-r--r-- 0 root (0) root (0) 68117 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/doc/Introduction_to_MutationalPatterns.Rmd │ │ │ --rw-r--r-- 0 root (0) root (0) 1724 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/doc/index.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 1317 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/doc/index.html │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/extdata/ │ │ │ -rw-r--r-- 0 root (0) root (0) 56311 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/extdata/ReplicationDirectionRegions.bed │ │ │ -rw-r--r-- 0 root (0) root (0) 486074 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/extdata/blood-AC.vcf │ │ │ -rw-r--r-- 0 root (0) root (0) 177118 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/extdata/blood-ACC55.vcf │ │ │ -rw-r--r-- 0 root (0) root (0) 90659 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/extdata/blood-BCH.vcf │ │ │ -rw-r--r-- 0 root (0) root (0) 158642 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/extdata/callableloci-sample.bed │ │ │ -rw-r--r-- 0 root (0) root (0) 18600 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/extdata/colon1-sample.vcf │ │ │ @@ -59,18 +58,18 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 59851 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/extdata/signatures/snv_SIGNAL_exposure.txt │ │ │ -rw-r--r-- 0 root (0) root (0) 47544 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/extdata/signatures/snv_SIGNAL_reference.txt │ │ │ -rw-r--r-- 0 root (0) root (0) 217231 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/extdata/signatures/snv_SIGNAL_tissue.txt │ │ │ -rw-r--r-- 0 root (0) root (0) 8408 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/extdata/signatures/snv_SPARSE_reference.txt │ │ │ -rw-r--r-- 0 root (0) root (0) 144005 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/extdata/signatures/tsb_snv_COSMIC_v3.1_reference.txt │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/help/ │ │ │ -rw-r--r-- 0 root (0) root (0) 3223 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/help/AnIndex │ │ │ --rw-r--r-- 0 root (0) root (0) 184902 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/help/MutationalPatterns.rdb │ │ │ --rw-r--r-- 0 root (0) root (0) 1918 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/help/MutationalPatterns.rdx │ │ │ +-rw-r--r-- 0 root (0) root (0) 187255 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/help/MutationalPatterns.rdb │ │ │ +-rw-r--r-- 0 root (0) root (0) 1915 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/help/MutationalPatterns.rdx │ │ │ -rw-r--r-- 0 root (0) root (0) 846 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/help/aliases.rds │ │ │ --rw-r--r-- 0 root (0) root (0) 876 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/help/paths.rds │ │ │ +-rw-r--r-- 0 root (0) root (0) 900 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/help/paths.rds │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 14070 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/html/00Index.html │ │ │ -rw-r--r-- 0 root (0) root (0) 2133 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/html/R.css │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/scripts/ │ │ │ -rw-r--r-- 0 root (0) root (0) 7826 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/scripts/Format_signatures.R │ │ │ -rw-r--r-- 0 root (0) root (0) 700 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/scripts/create_example_dbs.R │ │ │ -rw-r--r-- 0 root (0) root (0) 1841 2026-08-12 16:10:47.000000 ./usr/lib/R/site-library/MutationalPatterns/scripts/create_example_indels.R │ │ ├── ./usr/lib/R/site-library/MutationalPatterns/R/MutationalPatterns.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -550,15 +550,15 @@ │ │ │ │ "imports" = " element_point = "element_point", geom_curve = "geom_curve", " │ │ │ │ "imports" = " ScaleDiscrete = "ScaleDiscrete", GeomViolin = "GeomViolin", " │ │ │ │ "imports" = " GeomErrorbar = "GeomErrorbar", scale_alpha_manual = "scale_alpha_manual", " │ │ │ │ "imports" = " Guide = "Guide"), magrittr = c("%>%" = "%>%"), methods = c(setClass = "setClass"), " │ │ │ │ "imports" = " methods = c(setGeneric = "setGeneric"), methods = c(setMethod = "setMethod"), " │ │ │ │ "imports" = " pracma = c(lsqnonneg = "lsqnonneg"))" │ │ │ │ "lazydata" = "" │ │ │ │ - "path" = ""/home/moeller/Salsa/r-bioc-mutationalpatterns/debian/r-bioc-mutationalpatterns/usr/lib/R/site-library/MutationalPatterns"" │ │ │ │ + "path" = ""/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/debian/r-bioc-mutationalpatterns/usr/lib/R/site-library/MutationalPatterns"" │ │ │ │ "spec" = "c(name = "MutationalPatterns", version = "3.22.0")" │ │ │ │ } │ │ │ │ │ │ │ │ .__S3MethodsTable__. (environment) = │ │ │ │ { │ │ │ │ } │ │ ├── ./usr/lib/R/site-library/MutationalPatterns/R/MutationalPatterns.rdx │ │ │ ├── MutationalPatterns.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,658 +1,658 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$.__C__region_cossim │ │ │ │ │ [1] 0 446 │ │ │ │ │ │ │ │ │ │ $variables$.__NAMESPACE__. │ │ │ │ │ -[1] 9094 52 │ │ │ │ │ +[1] 9109 52 │ │ │ │ │ │ │ │ │ │ $variables$.__S3MethodsTable__. │ │ │ │ │ -[1] 9277 52 │ │ │ │ │ +[1] 9292 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__get_sim_tb:MutationalPatterns` │ │ │ │ │ -[1] 10718 52 │ │ │ │ │ +[1] 10733 52 │ │ │ │ │ │ │ │ │ │ $variables$`.__T__show:methods` │ │ │ │ │ -[1] 199080 52 │ │ │ │ │ +[1] 199095 52 │ │ │ │ │ │ │ │ │ │ $variables$.calc_chrom_ends │ │ │ │ │ -[1] 199132 1039 │ │ │ │ │ +[1] 199147 1039 │ │ │ │ │ │ │ │ │ │ $variables$.calculate_lesion_segregation_gr │ │ │ │ │ -[1] 200171 3879 │ │ │ │ │ +[1] 200186 3879 │ │ │ │ │ │ │ │ │ │ $variables$.calculate_mismatches │ │ │ │ │ -[1] 204050 2135 │ │ │ │ │ +[1] 204065 2135 │ │ │ │ │ │ │ │ │ │ $variables$.calculate_strand_switch │ │ │ │ │ -[1] 206185 552 │ │ │ │ │ +[1] 206200 552 │ │ │ │ │ │ │ │ │ │ $variables$.calculate_strand_switches │ │ │ │ │ -[1] 206737 735 │ │ │ │ │ +[1] 206752 735 │ │ │ │ │ │ │ │ │ │ $variables$.check_chroms │ │ │ │ │ -[1] 207472 3276 │ │ │ │ │ +[1] 207487 3276 │ │ │ │ │ │ │ │ │ │ $variables$.check_no_indels │ │ │ │ │ -[1] 210748 580 │ │ │ │ │ +[1] 210763 580 │ │ │ │ │ │ │ │ │ │ $variables$.check_no_indels_gr │ │ │ │ │ -[1] 211328 712 │ │ │ │ │ +[1] 211343 712 │ │ │ │ │ │ │ │ │ │ $variables$.check_no_multi_alts │ │ │ │ │ -[1] 212040 583 │ │ │ │ │ +[1] 212055 583 │ │ │ │ │ │ │ │ │ │ $variables$.check_no_multi_alts_gr │ │ │ │ │ -[1] 212623 721 │ │ │ │ │ +[1] 212638 721 │ │ │ │ │ │ │ │ │ │ $variables$.check_no_substitutions │ │ │ │ │ -[1] 213344 583 │ │ │ │ │ +[1] 213359 583 │ │ │ │ │ │ │ │ │ │ $variables$.check_no_substitutions_gr │ │ │ │ │ -[1] 213927 721 │ │ │ │ │ +[1] 213942 721 │ │ │ │ │ │ │ │ │ │ $variables$.cos_sim_matrix_exclself │ │ │ │ │ -[1] 214648 835 │ │ │ │ │ +[1] 214663 835 │ │ │ │ │ │ │ │ │ │ $variables$.count_dbs_contexts_gr │ │ │ │ │ -[1] 215483 1594 │ │ │ │ │ +[1] 215498 1594 │ │ │ │ │ │ │ │ │ │ $variables$.count_indel_contexts_gr │ │ │ │ │ -[1] 217077 2138 │ │ │ │ │ +[1] 217092 2138 │ │ │ │ │ │ │ │ │ │ $variables$.count_mbs_contexts_gr │ │ │ │ │ -[1] 219215 1364 │ │ │ │ │ +[1] 219230 1364 │ │ │ │ │ │ │ │ │ │ $variables$.create_dummy_limits │ │ │ │ │ -[1] 220579 788 │ │ │ │ │ +[1] 220594 788 │ │ │ │ │ │ │ │ │ │ $variables$.create_profile_comparison │ │ │ │ │ -[1] 221367 1181 │ │ │ │ │ +[1] 221382 1181 │ │ │ │ │ │ │ │ │ │ $variables$.determine_regional_similarity_chr │ │ │ │ │ -[1] 222548 5353 │ │ │ │ │ +[1] 222563 5353 │ │ │ │ │ │ │ │ │ │ $variables$.filter_seqlevels │ │ │ │ │ -[1] 227901 1766 │ │ │ │ │ +[1] 227916 1766 │ │ │ │ │ │ │ │ │ │ $variables$.find_potential_splice_site_muts │ │ │ │ │ -[1] 229667 934 │ │ │ │ │ +[1] 229682 934 │ │ │ │ │ │ │ │ │ │ $variables$.find_potential_splice_site_muts_strand │ │ │ │ │ -[1] 230601 880 │ │ │ │ │ +[1] 230616 880 │ │ │ │ │ │ │ │ │ │ $variables$.find_substitution │ │ │ │ │ -[1] 231481 455 │ │ │ │ │ +[1] 231496 455 │ │ │ │ │ │ │ │ │ │ $variables$.get_1bp_dels │ │ │ │ │ -[1] 231936 1305 │ │ │ │ │ +[1] 231951 1305 │ │ │ │ │ │ │ │ │ │ $variables$.get_1bp_ins │ │ │ │ │ -[1] 233241 1323 │ │ │ │ │ +[1] 233256 1323 │ │ │ │ │ │ │ │ │ │ $variables$.get_alt │ │ │ │ │ -[1] 234564 855 │ │ │ │ │ +[1] 234579 855 │ │ │ │ │ │ │ │ │ │ $variables$.get_big_dels │ │ │ │ │ -[1] 235419 3856 │ │ │ │ │ +[1] 235434 3856 │ │ │ │ │ │ │ │ │ │ $variables$.get_big_ins │ │ │ │ │ -[1] 239275 1343 │ │ │ │ │ +[1] 239290 1343 │ │ │ │ │ │ │ │ │ │ $variables$.get_cds_ranges │ │ │ │ │ -[1] 240618 2165 │ │ │ │ │ +[1] 240633 2165 │ │ │ │ │ │ │ │ │ │ $variables$.get_cds_sequences │ │ │ │ │ -[1] 242783 704 │ │ │ │ │ +[1] 242798 704 │ │ │ │ │ │ │ │ │ │ $variables$.get_cos_sim_ori_vs_rec │ │ │ │ │ -[1] 243487 476 │ │ │ │ │ +[1] 243502 476 │ │ │ │ │ │ │ │ │ │ $variables$.get_dbs_context_gr │ │ │ │ │ -[1] 243963 1938 │ │ │ │ │ +[1] 243978 1938 │ │ │ │ │ │ │ │ │ │ $variables$.get_extended_sequence │ │ │ │ │ -[1] 245901 1658 │ │ │ │ │ +[1] 245916 1658 │ │ │ │ │ │ │ │ │ │ $variables$.get_indel_context_gr │ │ │ │ │ -[1] 247559 1069 │ │ │ │ │ +[1] 247574 1069 │ │ │ │ │ │ │ │ │ │ $variables$.get_mut_type_gr │ │ │ │ │ -[1] 248628 1913 │ │ │ │ │ +[1] 248643 1913 │ │ │ │ │ │ │ │ │ │ $variables$.get_mutation_density_chrom │ │ │ │ │ -[1] 250541 1802 │ │ │ │ │ +[1] 250556 1802 │ │ │ │ │ │ │ │ │ │ $variables$.get_muts_region │ │ │ │ │ -[1] 252343 500 │ │ │ │ │ +[1] 252358 500 │ │ │ │ │ │ │ │ │ │ $variables$.get_oligo_contexts │ │ │ │ │ -[1] 252843 2095 │ │ │ │ │ +[1] 252858 2095 │ │ │ │ │ │ │ │ │ │ $variables$.get_ref │ │ │ │ │ -[1] 254938 851 │ │ │ │ │ +[1] 254953 851 │ │ │ │ │ │ │ │ │ │ $variables$.get_ref_codons │ │ │ │ │ -[1] 255789 1131 │ │ │ │ │ +[1] 255804 1131 │ │ │ │ │ │ │ │ │ │ $variables$.get_sig_star │ │ │ │ │ -[1] 256920 1127 │ │ │ │ │ +[1] 256935 1127 │ │ │ │ │ │ │ │ │ │ $variables$.get_splice_genelocs │ │ │ │ │ -[1] 258047 644 │ │ │ │ │ +[1] 258062 644 │ │ │ │ │ │ │ │ │ │ $variables$.get_splice_single_genelocs │ │ │ │ │ -[1] 258691 459 │ │ │ │ │ +[1] 258706 459 │ │ │ │ │ │ │ │ │ │ $variables$.get_splice_site_ranges │ │ │ │ │ -[1] 259150 533 │ │ │ │ │ +[1] 259165 533 │ │ │ │ │ │ │ │ │ │ $variables$.get_splice_site_ranges_gr │ │ │ │ │ -[1] 259683 1093 │ │ │ │ │ +[1] 259698 1093 │ │ │ │ │ │ │ │ │ │ $variables$.get_splice_site_sequences │ │ │ │ │ -[1] 260776 539 │ │ │ │ │ +[1] 260791 539 │ │ │ │ │ │ │ │ │ │ $variables$.get_strandedness_gr │ │ │ │ │ -[1] 261315 788 │ │ │ │ │ +[1] 261330 788 │ │ │ │ │ │ │ │ │ │ $variables$.get_strandedness_tb │ │ │ │ │ -[1] 262103 733 │ │ │ │ │ +[1] 262118 733 │ │ │ │ │ │ │ │ │ │ $variables$.get_x_axis_breaks │ │ │ │ │ -[1] 262836 668 │ │ │ │ │ +[1] 262851 668 │ │ │ │ │ │ │ │ │ │ $variables$.indel_count_n_repeats │ │ │ │ │ -[1] 263504 833 │ │ │ │ │ +[1] 263519 833 │ │ │ │ │ │ │ │ │ │ $variables$.indel_get_n_repeats │ │ │ │ │ -[1] 264337 541 │ │ │ │ │ +[1] 264352 541 │ │ │ │ │ │ │ │ │ │ $variables$.indel_get_n_repeats_left │ │ │ │ │ -[1] 264878 592 │ │ │ │ │ +[1] 264893 592 │ │ │ │ │ │ │ │ │ │ $variables$.indel_get_n_repeats_right │ │ │ │ │ -[1] 265470 495 │ │ │ │ │ +[1] 265485 495 │ │ │ │ │ │ │ │ │ │ $variables$.intersect_with_region │ │ │ │ │ -[1] 265965 1609 │ │ │ │ │ +[1] 265980 1609 │ │ │ │ │ │ │ │ │ │ $variables$.is_na │ │ │ │ │ -[1] 267574 338 │ │ │ │ │ +[1] 267589 338 │ │ │ │ │ │ │ │ │ │ $variables$.lengthen_mut_matrix_single_sample │ │ │ │ │ -[1] 267912 1061 │ │ │ │ │ +[1] 267927 1061 │ │ │ │ │ │ │ │ │ │ $variables$.merge_muts │ │ │ │ │ -[1] 268973 1192 │ │ │ │ │ +[1] 268988 1192 │ │ │ │ │ │ │ │ │ │ $variables$.mutate_codon │ │ │ │ │ -[1] 270165 331 │ │ │ │ │ +[1] 270180 331 │ │ │ │ │ │ │ │ │ │ $variables$.not_gr │ │ │ │ │ -[1] 270496 610 │ │ │ │ │ +[1] 270511 610 │ │ │ │ │ │ │ │ │ │ $variables$.not_gr_or_grl │ │ │ │ │ -[1] 271106 625 │ │ │ │ │ +[1] 271121 625 │ │ │ │ │ │ │ │ │ │ $variables$.packageName │ │ │ │ │ -[1] 271731 63 │ │ │ │ │ +[1] 271746 63 │ │ │ │ │ │ │ │ │ │ $variables$.plot_correlation_bootstrap_sample │ │ │ │ │ -[1] 271794 2129 │ │ │ │ │ +[1] 271809 2129 │ │ │ │ │ │ │ │ │ │ $variables$.plot_lesion_segregation_gg │ │ │ │ │ -[1] 273923 1782 │ │ │ │ │ +[1] 273938 1782 │ │ │ │ │ │ │ │ │ │ $variables$.plot_regional_similarity_gg │ │ │ │ │ -[1] 275705 3461 │ │ │ │ │ +[1] 275720 3461 │ │ │ │ │ │ │ │ │ │ $variables$.plot_sim_decay │ │ │ │ │ -[1] 279166 2541 │ │ │ │ │ +[1] 279181 2541 │ │ │ │ │ │ │ │ │ │ $variables$.potential_splice_site_damage │ │ │ │ │ -[1] 281707 1383 │ │ │ │ │ +[1] 281722 1383 │ │ │ │ │ │ │ │ │ │ $variables$.read_single_vcf_as_grange │ │ │ │ │ -[1] 283090 2826 │ │ │ │ │ +[1] 283105 2826 │ │ │ │ │ │ │ │ │ │ $variables$.remove_indels │ │ │ │ │ -[1] 285916 755 │ │ │ │ │ +[1] 285931 755 │ │ │ │ │ │ │ │ │ │ $variables$.remove_indels_gr │ │ │ │ │ -[1] 286671 343 │ │ │ │ │ +[1] 286686 343 │ │ │ │ │ │ │ │ │ │ $variables$.remove_multi_alts_variants │ │ │ │ │ -[1] 287014 765 │ │ │ │ │ +[1] 287029 765 │ │ │ │ │ │ │ │ │ │ $variables$.remove_multi_alts_variants_gr │ │ │ │ │ -[1] 287779 457 │ │ │ │ │ +[1] 287794 457 │ │ │ │ │ │ │ │ │ │ $variables$.remove_substitutions │ │ │ │ │ -[1] 288236 760 │ │ │ │ │ +[1] 288251 760 │ │ │ │ │ │ │ │ │ │ $variables$.remove_substitutions_gr │ │ │ │ │ -[1] 288996 356 │ │ │ │ │ +[1] 289011 356 │ │ │ │ │ │ │ │ │ │ $variables$.resample_mut_mat │ │ │ │ │ -[1] 289352 1132 │ │ │ │ │ +[1] 289367 1132 │ │ │ │ │ │ │ │ │ │ $variables$.river_create_context_matrix │ │ │ │ │ -[1] 290484 1186 │ │ │ │ │ +[1] 290499 1186 │ │ │ │ │ │ │ │ │ │ $variables$.river_create_lodes │ │ │ │ │ -[1] 291670 1388 │ │ │ │ │ +[1] 291685 1388 │ │ │ │ │ │ │ │ │ │ $variables$.river_plot_river │ │ │ │ │ -[1] 293058 2202 │ │ │ │ │ +[1] 293073 2202 │ │ │ │ │ │ │ │ │ │ $variables$.rl20_gspan │ │ │ │ │ -[1] 295260 2384 │ │ │ │ │ +[1] 295275 2384 │ │ │ │ │ │ │ │ │ │ $variables$.set_large_indels_as_5plus │ │ │ │ │ -[1] 297644 804 │ │ │ │ │ +[1] 297659 804 │ │ │ │ │ │ │ │ │ │ $variables$.single_context_damage_analysis │ │ │ │ │ -[1] 298448 2404 │ │ │ │ │ +[1] 298463 2404 │ │ │ │ │ │ │ │ │ │ $variables$.single_context_damage_analysis_strand │ │ │ │ │ -[1] 300852 1726 │ │ │ │ │ +[1] 300867 1726 │ │ │ │ │ │ │ │ │ │ $variables$.split_mbs_gr │ │ │ │ │ -[1] 302578 2811 │ │ │ │ │ +[1] 302593 2811 │ │ │ │ │ │ │ │ │ │ $variables$.split_muts_region_gr │ │ │ │ │ -[1] 305389 1293 │ │ │ │ │ +[1] 305404 1293 │ │ │ │ │ │ │ │ │ │ $variables$.strict_refit_backwards_selection_sample │ │ │ │ │ -[1] 306682 2304 │ │ │ │ │ +[1] 306697 2304 │ │ │ │ │ │ │ │ │ │ $variables$.strict_refit_best_subset_selection_sample │ │ │ │ │ -[1] 308986 1567 │ │ │ │ │ +[1] 309001 1567 │ │ │ │ │ │ │ │ │ │ $variables$.strict_refit_best_subset_selection_sample_n │ │ │ │ │ -[1] 310553 746 │ │ │ │ │ +[1] 310568 746 │ │ │ │ │ │ │ │ │ │ $variables$.strict_refit_best_subset_selection_single_set │ │ │ │ │ -[1] 311299 515 │ │ │ │ │ +[1] 311314 515 │ │ │ │ │ │ │ │ │ │ $variables$.subsample_granges │ │ │ │ │ -[1] 311814 537 │ │ │ │ │ +[1] 311829 537 │ │ │ │ │ │ │ │ │ │ $variables$.wald_wolfowitz_test │ │ │ │ │ -[1] 312351 1445 │ │ │ │ │ +[1] 312366 1445 │ │ │ │ │ │ │ │ │ │ $variables$COLORS6 │ │ │ │ │ -[1] 313796 85 │ │ │ │ │ +[1] 313811 85 │ │ │ │ │ │ │ │ │ │ $variables$COLORS7 │ │ │ │ │ -[1] 313881 92 │ │ │ │ │ +[1] 313896 92 │ │ │ │ │ │ │ │ │ │ $variables$CONTEXTS_96 │ │ │ │ │ -[1] 313973 117 │ │ │ │ │ +[1] 313988 117 │ │ │ │ │ │ │ │ │ │ $variables$C_TRIPLETS │ │ │ │ │ -[1] 314090 84 │ │ │ │ │ +[1] 314105 84 │ │ │ │ │ │ │ │ │ │ $variables$DBS_CATEGORIES │ │ │ │ │ -[1] 314174 266 │ │ │ │ │ +[1] 314189 266 │ │ │ │ │ │ │ │ │ │ $variables$DBS_COLORS │ │ │ │ │ -[1] 314440 110 │ │ │ │ │ +[1] 314455 110 │ │ │ │ │ │ │ │ │ │ $variables$DNA_BASES │ │ │ │ │ -[1] 314550 53 │ │ │ │ │ +[1] 314565 53 │ │ │ │ │ │ │ │ │ │ $variables$INDEL_CATEGORIES │ │ │ │ │ -[1] 314603 299 │ │ │ │ │ +[1] 314618 299 │ │ │ │ │ │ │ │ │ │ $variables$INDEL_COLORS │ │ │ │ │ -[1] 314902 138 │ │ │ │ │ +[1] 314917 138 │ │ │ │ │ │ │ │ │ │ $variables$MBS_CATEGORIES │ │ │ │ │ -[1] 315040 154 │ │ │ │ │ +[1] 315055 154 │ │ │ │ │ │ │ │ │ │ $variables$MBS_COLORS │ │ │ │ │ -[1] 315194 97 │ │ │ │ │ +[1] 315209 97 │ │ │ │ │ │ │ │ │ │ $variables$STRAND │ │ │ │ │ -[1] 315291 65 │ │ │ │ │ +[1] 315306 65 │ │ │ │ │ │ │ │ │ │ $variables$SUBSTITUTIONS │ │ │ │ │ -[1] 315356 63 │ │ │ │ │ +[1] 315371 63 │ │ │ │ │ │ │ │ │ │ $variables$SUBSTITUTIONS_192 │ │ │ │ │ -[1] 315419 81 │ │ │ │ │ +[1] 315434 81 │ │ │ │ │ │ │ │ │ │ $variables$SUBSTITUTIONS_96 │ │ │ │ │ -[1] 315500 75 │ │ │ │ │ +[1] 315515 75 │ │ │ │ │ │ │ │ │ │ $variables$TRIPLETS_96 │ │ │ │ │ -[1] 315575 233 │ │ │ │ │ +[1] 315590 233 │ │ │ │ │ │ │ │ │ │ $variables$T_TRIPLETS │ │ │ │ │ -[1] 315808 84 │ │ │ │ │ +[1] 315823 84 │ │ │ │ │ │ │ │ │ │ $variables$bin_mutation_density │ │ │ │ │ -[1] 315892 1703 │ │ │ │ │ +[1] 315907 1703 │ │ │ │ │ │ │ │ │ │ $variables$binomial_test │ │ │ │ │ -[1] 317595 1048 │ │ │ │ │ +[1] 317610 1048 │ │ │ │ │ │ │ │ │ │ $variables$calculate_lesion_segregation │ │ │ │ │ -[1] 318643 2409 │ │ │ │ │ +[1] 318658 2409 │ │ │ │ │ │ │ │ │ │ $variables$cluster_signatures │ │ │ │ │ -[1] 321052 506 │ │ │ │ │ +[1] 321067 506 │ │ │ │ │ │ │ │ │ │ $variables$context_potential_damage_analysis │ │ │ │ │ -[1] 321558 3579 │ │ │ │ │ +[1] 321573 3579 │ │ │ │ │ │ │ │ │ │ $variables$convert_sigs_to_ref │ │ │ │ │ -[1] 325137 1450 │ │ │ │ │ +[1] 325152 1450 │ │ │ │ │ │ │ │ │ │ $variables$cos_sim │ │ │ │ │ -[1] 326587 429 │ │ │ │ │ +[1] 326602 429 │ │ │ │ │ │ │ │ │ │ $variables$cos_sim_matrix │ │ │ │ │ -[1] 327016 1474 │ │ │ │ │ +[1] 327031 1474 │ │ │ │ │ │ │ │ │ │ $variables$count_dbs_contexts │ │ │ │ │ -[1] 328490 1568 │ │ │ │ │ +[1] 328505 1568 │ │ │ │ │ │ │ │ │ │ $variables$count_indel_contexts │ │ │ │ │ -[1] 330058 1571 │ │ │ │ │ +[1] 330073 1571 │ │ │ │ │ │ │ │ │ │ $variables$count_mbs_contexts │ │ │ │ │ -[1] 331629 1343 │ │ │ │ │ +[1] 331644 1343 │ │ │ │ │ │ │ │ │ │ $variables$determine_regional_similarity │ │ │ │ │ -[1] 332972 3908 │ │ │ │ │ +[1] 332987 3908 │ │ │ │ │ │ │ │ │ │ $variables$enrichment_depletion_test │ │ │ │ │ -[1] 336880 2690 │ │ │ │ │ +[1] 336895 2690 │ │ │ │ │ │ │ │ │ │ $variables$extract_signatures │ │ │ │ │ -[1] 339570 2311 │ │ │ │ │ +[1] 339585 2311 │ │ │ │ │ │ │ │ │ │ $variables$fit_to_signatures │ │ │ │ │ -[1] 341881 1894 │ │ │ │ │ +[1] 341896 1894 │ │ │ │ │ │ │ │ │ │ $variables$fit_to_signatures_bootstrapped │ │ │ │ │ -[1] 343775 3381 │ │ │ │ │ +[1] 343790 3381 │ │ │ │ │ │ │ │ │ │ $variables$fit_to_signatures_strict │ │ │ │ │ -[1] 347156 3103 │ │ │ │ │ +[1] 347171 3103 │ │ │ │ │ │ │ │ │ │ $variables$genomic_distribution │ │ │ │ │ -[1] 350259 1431 │ │ │ │ │ +[1] 350274 1431 │ │ │ │ │ │ │ │ │ │ $variables$get_dbs_context │ │ │ │ │ -[1] 351690 1255 │ │ │ │ │ +[1] 351705 1255 │ │ │ │ │ │ │ │ │ │ $variables$get_indel_context │ │ │ │ │ -[1] 352945 1334 │ │ │ │ │ +[1] 352960 1334 │ │ │ │ │ │ │ │ │ │ $variables$get_known_signatures │ │ │ │ │ -[1] 354279 3965 │ │ │ │ │ +[1] 354294 3965 │ │ │ │ │ │ │ │ │ │ $variables$get_mut_type │ │ │ │ │ -[1] 358244 1288 │ │ │ │ │ +[1] 358259 1288 │ │ │ │ │ │ │ │ │ │ $variables$get_sim_tb │ │ │ │ │ -[1] 359532 406 │ │ │ │ │ +[1] 359547 406 │ │ │ │ │ │ │ │ │ │ $variables$lengthen_mut_matrix │ │ │ │ │ -[1] 359938 1355 │ │ │ │ │ +[1] 359953 1355 │ │ │ │ │ │ │ │ │ │ $variables$merge_signatures │ │ │ │ │ -[1] 361293 2358 │ │ │ │ │ +[1] 361308 2358 │ │ │ │ │ │ │ │ │ │ $variables$mut_192_occurrences │ │ │ │ │ -[1] 363651 2355 │ │ │ │ │ +[1] 363666 2355 │ │ │ │ │ │ │ │ │ │ $variables$mut_96_occurrences │ │ │ │ │ -[1] 366006 3173 │ │ │ │ │ +[1] 366021 3173 │ │ │ │ │ │ │ │ │ │ $variables$mut_context │ │ │ │ │ -[1] 369179 685 │ │ │ │ │ +[1] 369194 685 │ │ │ │ │ │ │ │ │ │ $variables$mut_matrix │ │ │ │ │ -[1] 369864 1151 │ │ │ │ │ +[1] 369879 1151 │ │ │ │ │ │ │ │ │ │ $variables$mut_matrix_stranded │ │ │ │ │ -[1] 371015 1231 │ │ │ │ │ +[1] 371030 1231 │ │ │ │ │ │ │ │ │ │ $variables$mut_strand │ │ │ │ │ -[1] 372246 4809 │ │ │ │ │ +[1] 372261 4809 │ │ │ │ │ │ │ │ │ │ $variables$mut_type │ │ │ │ │ -[1] 377055 652 │ │ │ │ │ +[1] 377070 652 │ │ │ │ │ │ │ │ │ │ $variables$mut_type_occurrences │ │ │ │ │ -[1] 377707 2898 │ │ │ │ │ +[1] 377722 2898 │ │ │ │ │ │ │ │ │ │ $variables$mutations_from_vcf │ │ │ │ │ -[1] 380605 567 │ │ │ │ │ +[1] 380620 567 │ │ │ │ │ │ │ │ │ │ $variables$plot_192_profile │ │ │ │ │ -[1] 381172 3958 │ │ │ │ │ +[1] 381187 3958 │ │ │ │ │ │ │ │ │ │ $variables$plot_96_profile │ │ │ │ │ -[1] 385130 3259 │ │ │ │ │ +[1] 385145 3259 │ │ │ │ │ │ │ │ │ │ $variables$plot_bootstrapped_contribution │ │ │ │ │ -[1] 388389 4936 │ │ │ │ │ +[1] 388404 4936 │ │ │ │ │ │ │ │ │ │ $variables$plot_compare_dbs │ │ │ │ │ -[1] 393325 3331 │ │ │ │ │ +[1] 393340 3331 │ │ │ │ │ │ │ │ │ │ $variables$plot_compare_indels │ │ │ │ │ -[1] 396656 2747 │ │ │ │ │ +[1] 396671 2747 │ │ │ │ │ │ │ │ │ │ $variables$plot_compare_mbs │ │ │ │ │ -[1] 399403 2430 │ │ │ │ │ +[1] 399418 2430 │ │ │ │ │ │ │ │ │ │ $variables$plot_compare_profiles │ │ │ │ │ -[1] 401833 3318 │ │ │ │ │ +[1] 401848 3318 │ │ │ │ │ │ │ │ │ │ $variables$plot_contribution │ │ │ │ │ -[1] 405151 2995 │ │ │ │ │ +[1] 405166 2995 │ │ │ │ │ │ │ │ │ │ $variables$plot_contribution_heatmap │ │ │ │ │ -[1] 408146 5732 │ │ │ │ │ +[1] 408161 5732 │ │ │ │ │ │ │ │ │ │ $variables$plot_correlation_bootstrap │ │ │ │ │ -[1] 413878 1198 │ │ │ │ │ +[1] 413893 1198 │ │ │ │ │ │ │ │ │ │ $variables$plot_cosine_heatmap │ │ │ │ │ -[1] 415076 5745 │ │ │ │ │ +[1] 415091 5745 │ │ │ │ │ │ │ │ │ │ $variables$plot_dbs_contexts │ │ │ │ │ -[1] 420821 3647 │ │ │ │ │ +[1] 420836 3647 │ │ │ │ │ │ │ │ │ │ $variables$plot_enrichment_depletion │ │ │ │ │ -[1] 424468 3931 │ │ │ │ │ +[1] 424483 3931 │ │ │ │ │ │ │ │ │ │ $variables$plot_indel_contexts │ │ │ │ │ -[1] 428399 3433 │ │ │ │ │ +[1] 428414 3433 │ │ │ │ │ │ │ │ │ │ $variables$plot_lesion_segregation │ │ │ │ │ -[1] 431832 6179 │ │ │ │ │ +[1] 431847 6179 │ │ │ │ │ │ │ │ │ │ $variables$plot_main_dbs_contexts │ │ │ │ │ -[1] 438011 2863 │ │ │ │ │ +[1] 438026 2863 │ │ │ │ │ │ │ │ │ │ $variables$plot_main_indel_contexts │ │ │ │ │ -[1] 440874 2855 │ │ │ │ │ +[1] 440889 2855 │ │ │ │ │ │ │ │ │ │ $variables$plot_mbs_contexts │ │ │ │ │ -[1] 443729 2272 │ │ │ │ │ +[1] 443744 2272 │ │ │ │ │ │ │ │ │ │ $variables$plot_original_vs_reconstructed │ │ │ │ │ -[1] 446001 1471 │ │ │ │ │ +[1] 446016 1471 │ │ │ │ │ │ │ │ │ │ $variables$plot_profile_heatmap │ │ │ │ │ -[1] 447472 5374 │ │ │ │ │ +[1] 447487 5374 │ │ │ │ │ │ │ │ │ │ $variables$plot_profile_region │ │ │ │ │ -[1] 452846 5000 │ │ │ │ │ +[1] 452861 5000 │ │ │ │ │ │ │ │ │ │ $variables$plot_rainfall │ │ │ │ │ -[1] 457846 6960 │ │ │ │ │ +[1] 457861 6960 │ │ │ │ │ │ │ │ │ │ $variables$plot_regional_similarity │ │ │ │ │ -[1] 464806 2817 │ │ │ │ │ +[1] 464821 2817 │ │ │ │ │ │ │ │ │ │ $variables$plot_river │ │ │ │ │ -[1] 467623 472 │ │ │ │ │ +[1] 467638 472 │ │ │ │ │ │ │ │ │ │ $variables$plot_signature_strand_bias │ │ │ │ │ -[1] 468095 3907 │ │ │ │ │ +[1] 468110 3907 │ │ │ │ │ │ │ │ │ │ $variables$plot_spectrum │ │ │ │ │ -[1] 472002 6844 │ │ │ │ │ +[1] 472017 6844 │ │ │ │ │ │ │ │ │ │ $variables$plot_spectrum_region │ │ │ │ │ -[1] 478846 7516 │ │ │ │ │ +[1] 478861 7516 │ │ │ │ │ │ │ │ │ │ $variables$plot_strand │ │ │ │ │ -[1] 486362 2033 │ │ │ │ │ +[1] 486377 2033 │ │ │ │ │ │ │ │ │ │ $variables$plot_strand_bias │ │ │ │ │ -[1] 488395 3439 │ │ │ │ │ +[1] 488410 3439 │ │ │ │ │ │ │ │ │ │ $variables$pool_mut_mat │ │ │ │ │ -[1] 491834 967 │ │ │ │ │ +[1] 491849 967 │ │ │ │ │ │ │ │ │ │ $variables$read_vcfs_as_granges │ │ │ │ │ -[1] 492801 1482 │ │ │ │ │ +[1] 492816 1482 │ │ │ │ │ │ │ │ │ │ $variables$rename_nmf_signatures │ │ │ │ │ -[1] 494283 2171 │ │ │ │ │ +[1] 494298 2171 │ │ │ │ │ │ │ │ │ │ $variables$signature_potential_damage_analysis │ │ │ │ │ -[1] 496454 2474 │ │ │ │ │ +[1] 496469 2474 │ │ │ │ │ │ │ │ │ │ $variables$split_muts_region │ │ │ │ │ -[1] 498928 1723 │ │ │ │ │ +[1] 498943 1723 │ │ │ │ │ │ │ │ │ │ $variables$strand_bias_test │ │ │ │ │ -[1] 500651 1882 │ │ │ │ │ +[1] 500666 1882 │ │ │ │ │ │ │ │ │ │ $variables$strand_occurrences │ │ │ │ │ -[1] 502533 2054 │ │ │ │ │ +[1] 502548 2054 │ │ │ │ │ │ │ │ │ │ $variables$type_context │ │ │ │ │ -[1] 504587 1309 │ │ │ │ │ +[1] 504602 1309 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 745 8349 │ │ │ │ │ +[1] 745 8364 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 197709 459 │ │ │ │ │ +[1] 197724 459 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 126007 35851 │ │ │ │ │ +[1] 126022 35851 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 10770 170 │ │ │ │ │ +[1] 10785 170 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 10940 1515 │ │ │ │ │ +[1] 10955 1515 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 123533 2474 │ │ │ │ │ +[1] 123548 2474 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 109089 143 │ │ │ │ │ +[1] 109104 143 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 103963 5126 │ │ │ │ │ +[1] 103978 5126 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 103241 722 │ │ │ │ │ +[1] 103256 722 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 21192 143 │ │ │ │ │ +[1] 21207 143 │ │ │ │ │ │ │ │ │ │ $references$`env::19` │ │ │ │ │ -[1] 12455 8737 │ │ │ │ │ +[1] 12470 8737 │ │ │ │ │ │ │ │ │ │ $references$`env::2` │ │ │ │ │ [1] 446 131 │ │ │ │ │ │ │ │ │ │ $references$`env::20` │ │ │ │ │ -[1] 98482 4759 │ │ │ │ │ +[1] 98497 4759 │ │ │ │ │ │ │ │ │ │ $references$`env::21` │ │ │ │ │ -[1] 37190 37398 │ │ │ │ │ +[1] 37205 37398 │ │ │ │ │ │ │ │ │ │ $references$`env::22` │ │ │ │ │ -[1] 29432 336 │ │ │ │ │ +[1] 29447 336 │ │ │ │ │ │ │ │ │ │ $references$`env::23` │ │ │ │ │ -[1] 22426 7006 │ │ │ │ │ +[1] 22441 7006 │ │ │ │ │ │ │ │ │ │ $references$`env::24` │ │ │ │ │ -[1] 21335 1091 │ │ │ │ │ +[1] 21350 1091 │ │ │ │ │ │ │ │ │ │ $references$`env::25` │ │ │ │ │ -[1] 29768 2269 │ │ │ │ │ +[1] 29783 2269 │ │ │ │ │ │ │ │ │ │ $references$`env::26` │ │ │ │ │ -[1] 32037 4845 │ │ │ │ │ +[1] 32052 4845 │ │ │ │ │ │ │ │ │ │ $references$`env::27` │ │ │ │ │ -[1] 36882 308 │ │ │ │ │ +[1] 36897 308 │ │ │ │ │ │ │ │ │ │ $references$`env::28` │ │ │ │ │ -[1] 74588 23894 │ │ │ │ │ +[1] 74603 23894 │ │ │ │ │ │ │ │ │ │ $references$`env::29` │ │ │ │ │ -[1] 115025 2511 │ │ │ │ │ +[1] 115040 2511 │ │ │ │ │ │ │ │ │ │ $references$`env::3` │ │ │ │ │ [1] 577 168 │ │ │ │ │ │ │ │ │ │ $references$`env::30` │ │ │ │ │ -[1] 114866 159 │ │ │ │ │ +[1] 114881 159 │ │ │ │ │ │ │ │ │ │ $references$`env::31` │ │ │ │ │ -[1] 109232 5634 │ │ │ │ │ +[1] 109247 5634 │ │ │ │ │ │ │ │ │ │ $references$`env::32` │ │ │ │ │ -[1] 123390 143 │ │ │ │ │ +[1] 123405 143 │ │ │ │ │ │ │ │ │ │ $references$`env::33` │ │ │ │ │ -[1] 118259 5131 │ │ │ │ │ +[1] 118274 5131 │ │ │ │ │ │ │ │ │ │ $references$`env::34` │ │ │ │ │ -[1] 117536 723 │ │ │ │ │ +[1] 117551 723 │ │ │ │ │ │ │ │ │ │ $references$`env::35` │ │ │ │ │ -[1] 161858 35851 │ │ │ │ │ +[1] 161873 35851 │ │ │ │ │ │ │ │ │ │ $references$`env::4` │ │ │ │ │ -[1] 9146 131 │ │ │ │ │ +[1] 9161 131 │ │ │ │ │ │ │ │ │ │ $references$`env::5` │ │ │ │ │ -[1] 10343 375 │ │ │ │ │ +[1] 10358 375 │ │ │ │ │ │ │ │ │ │ $references$`env::6` │ │ │ │ │ -[1] 10079 264 │ │ │ │ │ +[1] 10094 264 │ │ │ │ │ │ │ │ │ │ $references$`env::7` │ │ │ │ │ -[1] 9329 375 │ │ │ │ │ +[1] 9344 375 │ │ │ │ │ │ │ │ │ │ $references$`env::8` │ │ │ │ │ -[1] 9704 375 │ │ │ │ │ +[1] 9719 375 │ │ │ │ │ │ │ │ │ │ $references$`env::9` │ │ │ │ │ -[1] 198168 912 │ │ │ │ │ +[1] 198183 912 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/MutationalPatterns/doc/index.html │ │ │ @@ -10,28 +10,17 @@ │ │ │ │ │ │
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Vignettes from package 'MutationalPatterns'

│ │ │ - │ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ -│ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ - │ │ │ -
MutationalPatterns::Introduction to MutationalPatternssource
│ │ │ +The package contains no vignette meta-information. │ │ │

Other files in the doc directory

│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ + │ │ │
Introduction_to_MutationalPatterns.R
Introduction_to_MutationalPatterns.Rmd
│ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -1,7 +1,8 @@ │ │ │ │ ************ VViiggnneetttteess aanndd ootthheerr ddooccuummeennttaattiioonn[[[[RR llooggoo]]]] ************ │ │ │ │ =============================================================================== │ │ │ │ _[_[_U_p_]_]_[_[_T_o_p_]_] │ │ │ │ ********** VViiggnneetttteess ffrroomm ppaacckkaaggee ''MMuuttaattiioonnaallPPaatttteerrnnss'' ********** │ │ │ │ -_M_u_t_a_t_i_o_n_a_l_P_a_t_t_e_r_n_s_:_: Introduction to MutationalPatterns _s_o_u_r_c_e │ │ │ │ +The package contains no vignette meta-information. │ │ │ │ ********** OOtthheerr ffiilleess iinn tthhee ddoocc ddiirreeccttoorryy ********** │ │ │ │ _I_n_t_r_o_d_u_c_t_i_o_n___t_o___M_u_t_a_t_i_o_n_a_l_P_a_t_t_e_r_n_s_._R │ │ │ │ + _I_n_t_r_o_d_u_c_t_i_o_n___t_o___M_u_t_a_t_i_o_n_a_l_P_a_t_t_e_r_n_s_._R_m_d │ │ ├── ./usr/lib/R/site-library/MutationalPatterns/help/MutationalPatterns.rdb │ │ │ ├── Rscript --vanilla - {} │ │ │ │ @@ -10,15 +10,15 @@ │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure("mutation_context", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", \n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("mutation_types", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", \n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("strand_from_vcf", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(", \n", Rd_tag = "TEXT"), structure(" ", Rd_tag = "TEXT"), │ │ │ │ structure(list(structure("explained_by_signatures", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/MutationalPatterns-defunct.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\details")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/MutationalPatterns-defunct.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ MutationalPatterns-package (list) = structure(list(structure(list(structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure("MutationalPatterns: an integrative R package for studying patterns in\n", Rd_tag = "TEXT"), │ │ │ │ structure("base substitution catalogues\n", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("MutationalPatterns", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("MutationalPatterns-package", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ @@ -59,15 +59,15 @@ │ │ │ │ structure("human cancers. Nat. Rev. Genet., 15, 585–598.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("Lawrence,M. et al. (2013) Software for computing and annotating genomic\n", Rd_tag = "TEXT"), │ │ │ │ structure("ranges. PLoS Comput. Biol., 9, e1003118.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("Pleasance,E.D. et al. (2010) A comprehensive catalogue of somatic\n", Rd_tag = "TEXT"), │ │ │ │ structure("mutations from a human cancer genome. Nature, 463, 191–196.\n", Rd_tag = "TEXT")), Rd_tag = "\\references"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("https://github.com/CuppenResearch/MutationalPatterns", Rd_tag = "VERB")), Rd_tag = "\\url"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/MutationalPatterns-package.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/MutationalPatterns-package.Rd", class = "Rd", meta = list( │ │ │ │ docType = "package", generator = ""), prepared = 3L) │ │ │ │ │ │ │ │ bin_mutation_density (list) = structure(list(structure(list(structure("Bin the genome based on mutation density", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("bin_mutation_density", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("bin_mutation_density", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("genomic_regions", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function splits the genome based on the mutation density.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -117,15 +117,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Determine region density\n", Rd_tag = "RCODE"), │ │ │ │ structure("dens_grl <- bin_mutation_density(grl, ref_genome, nrbins = 3)\n", Rd_tag = "RCODE"), │ │ │ │ structure("names(dens_grl) <- c(\"Low\", \"Medium\", \"High\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## You can also use manual cutoffs. This feature is meant for more\n", Rd_tag = "RCODE"), │ │ │ │ structure("## advanced users. It can be usefull if you want to find highly mutated regions, with\n", Rd_tag = "RCODE"), │ │ │ │ structure("## a consistent cutoff between analyses.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("dens_grl_man <- bin_mutation_density(grl, ref_genome, man_dens_cutoffs = c(0, 2e-08, 1))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/bin_mutation_density.Rd", class = "Rd", meta = list( │ │ │ │ + structure("dens_grl_man <- bin_mutation_density(grl, ref_genome, man_dens_cutoffs = c(0, 2e-08, 1))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/bin_mutation_density.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ binomial_test (list) = structure(list(structure(list(structure("Binomial test for enrichment or depletion testing", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("binomial_test", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("binomial_test", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function performs lower-tail binomial test for depletion and\n", Rd_tag = "TEXT"), │ │ │ │ structure("upper-tail test for enrichment\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -141,15 +141,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("p_cutoffs", Rd_tag = "TEXT")), │ │ │ │ list(structure("Significance cutoff for the p value. Default: 0.05", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A data.frame with direction of effect (enrichment/depletion),\n", Rd_tag = "TEXT"), │ │ │ │ structure("P-value and significance asterisks\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("binomial_test(0.5, 1200, 543)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("binomial_test(0.2, 800, 150)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/binomial_test.Rd", class = "Rd", meta = list( │ │ │ │ + structure("binomial_test(0.2, 800, 150)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/binomial_test.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ calculate_lesion_segregation (list) = structure(list(structure(list(structure("Calculate the amount of lesion segregation for a GRangesList or GRanges object.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("calculate_lesion_segregation", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("calculate_lesion_segregation", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Lesion_segregation", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function calculates lesion segregation for a GRangesList or GRanges object.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -239,15 +239,15 @@ │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Calculate lesion segregation using the rl20.\n", Rd_tag = "RCODE"), │ │ │ │ structure("chromosomes <- paste0(\"chr\", c(1:22, \"X\"))\n", Rd_tag = "RCODE"), │ │ │ │ structure("lesion_segregation_rl20 <- calculate_lesion_segregation(grl,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" sample_names,\n", Rd_tag = "RCODE"), structure(" test = \"rl20\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" ref_genome = ref_genome,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" chromosomes = chromosomes\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/calculate_lesion_segregation.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/calculate_lesion_segregation.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ cluster_signatures (list) = structure(list(structure(list(structure("Signature clustering function", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("cluster_signatures", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("cluster_signatures", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Hierarchical clustering of signatures based on cosine similarity\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("cluster_signatures(signatures, method = \"complete\")\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -271,15 +271,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## See the 'mut_matrix()' example for how we obtained the mutation matrix:\n", Rd_tag = "RCODE"), │ │ │ │ structure("mut_mat <- readRDS(system.file(\"states/mut_mat_data.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Hierarchically cluster the cancer signatures based on cosine similarity\n", Rd_tag = "RCODE"), │ │ │ │ structure("hclust_signatures <- cluster_signatures(signatures)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Plot dendrogram\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot(hclust_signatures)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/cluster_signatures.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot(hclust_signatures)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/cluster_signatures.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ context_potential_damage_analysis (list) = structure(list(structure(list(structure("Potential damage analysis for the supplied mutational contexts", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("context_potential_damage_analysis", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("context_potential_damage_analysis", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The ratio of possible 'stop gain', 'mismatches', 'synonymous mutations' and\n", Rd_tag = "TEXT"), │ │ │ │ structure("'splice site mutations' is counted per mutational context. This is done for\n", Rd_tag = "TEXT"), │ │ │ │ @@ -356,15 +356,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Run the function\n", Rd_tag = "RCODE"), │ │ │ │ structure("context_potential_damage_analysis(contexts, txdb, ref_genome, gene_ids)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## The function can provide updates about its progress.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## This can be usefull when it's running slowly,\n", Rd_tag = "RCODE"), │ │ │ │ structure("## which can happen when you are using many gene_ids.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## To reduce the example runtime, we don't re-run the analysis, but only show the command\n", Rd_tag = "RCODE"), │ │ │ │ structure("## context_potential_damage_analysis(contexts, txdb, ref_genome, gene_ids, verbose = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/context_potential_damage_analysis.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/context_potential_damage_analysis.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ convert_sigs_to_ref (list) = structure(list(structure(list(structure("Convert tissue specific signature exposures to reference", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("convert_sigs_to_ref", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("convert_sigs_to_ref", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function converts tissue specific signature contributions into\n", Rd_tag = "TEXT"), │ │ │ │ structure("reference signature contributions. This works on SNV signatures from SIGNAL.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -382,15 +382,15 @@ │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Get tissue specific signatures\n", Rd_tag = "RCODE"), │ │ │ │ structure("signatures <- get_known_signatures(source = \"SIGNAL\", sig_type = \"tissue\", tissue_type = \"Skin\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Fit tissue specific signatures\n", Rd_tag = "RCODE"), │ │ │ │ structure("fit_res <- fit_to_signatures(mut_mat, signatures)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Convert the tissue specific signatures exposures to reference\n", Rd_tag = "RCODE"), │ │ │ │ - structure("fit_res <- convert_sigs_to_ref(fit_res)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/convert_sigs_to_ref.Rd", class = "Rd", meta = list( │ │ │ │ + structure("fit_res <- convert_sigs_to_ref(fit_res)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/convert_sigs_to_ref.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ cos_sim (list) = structure(list(structure(list(structure("Cosine similarity function", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("cos_sim", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("cos_sim", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the cosine similarity between two vectors of the same length.\n", Rd_tag = "TEXT"), │ │ │ │ structure("The cosine similarity is a value between 0 (distinct) and 1 (identical)\n", Rd_tag = "TEXT"), │ │ │ │ @@ -401,15 +401,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("y", Rd_tag = "TEXT")), │ │ │ │ list(structure("Vector 2 of length n", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Cosine similarity value; a value between 0 and 1\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("x <- c(1.1, 2.1, 0.2, 0.1, 2.9)\n", Rd_tag = "RCODE"), │ │ │ │ structure("y <- c(0.9, 1.9, 0.5, 0.4, 3.1)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("cos_sim(x, y)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/cos_sim.Rd", class = "Rd", meta = list( │ │ │ │ + structure("cos_sim(x, y)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/cos_sim.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ cos_sim_matrix (list) = structure(list(structure(list(structure("Compute all pairwise cosine similarities between mutational profiles/signatures", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("cos_sim_matrix", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("cos_sim_matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Computes all pairwise cosine similarities between the mutational profiles provided in the two mutation count matrices.\n", Rd_tag = "TEXT"), │ │ │ │ structure("The cosine similarity is a value between 0 (distinct) and 1 (identical) and indicates how much two vectors are alike.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -432,15 +432,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## Get signatures\n", Rd_tag = "RCODE"), │ │ │ │ structure("signatures <- get_known_signatures()\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## See the 'mut_matrix()' example for how we obtained the mutation matrix:\n", Rd_tag = "RCODE"), │ │ │ │ structure("mut_mat <- readRDS(system.file(\"states/mut_mat_data.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Calculate the cosine similarity between each COSMIC signature and each 96 mutational profile\n", Rd_tag = "RCODE"), │ │ │ │ - structure("cos_sim_matrix(mut_mat, signatures)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/cos_sim_matrix.Rd", class = "Rd", meta = list( │ │ │ │ + structure("cos_sim_matrix(mut_mat, signatures)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/cos_sim_matrix.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ count_dbs_contexts (list) = structure(list(structure(list(structure("Count DBS contexts", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("count_dbs_contexts", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("count_dbs_contexts", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("DBS", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Count DBS contexts\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -470,15 +470,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## Get a GRangesList or GRanges object with DBS contexts.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## See 'dbs_get_context' for more info on how to do this.\n", Rd_tag = "RCODE"), │ │ │ │ structure("grl_dbs_context <- readRDS(system.file(\"states/blood_grl_dbs_context.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Count the DBS contexts\n", Rd_tag = "RCODE"), │ │ │ │ - structure("count_dbs_contexts(grl_dbs_context)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/count_dbs_contexts.Rd", class = "Rd", meta = list( │ │ │ │ + structure("count_dbs_contexts(grl_dbs_context)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/count_dbs_contexts.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ count_indel_contexts (list) = structure(list(structure(list(structure("Count indel contexts", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("count_indel_contexts", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("count_indel_contexts", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Indels", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Count indel contexts\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -508,15 +508,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## Get a GRangesList or GRanges object with indel contexts.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## See 'indel_get_context' for more info on how to do this.\n", Rd_tag = "RCODE"), │ │ │ │ structure("grl_indel_context <- readRDS(system.file(\"states/blood_grl_indel_context.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("# Count the indel contexts\n", Rd_tag = "RCODE"), │ │ │ │ - structure("count_indel_contexts(grl_indel_context)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/count_indel_contexts.Rd", class = "Rd", meta = list( │ │ │ │ + structure("count_indel_contexts(grl_indel_context)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/count_indel_contexts.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ count_mbs_contexts (list) = structure(list(structure(list(structure("Count MBS variants grouped by length.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("count_mbs_contexts", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("count_mbs_contexts", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("MBS", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Count MBS variants grouped by length.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -536,15 +536,15 @@ │ │ │ │ structure("plot_mbs_contexts", Rd_tag = "TEXT")), Rd_tag = "\\link"), │ │ │ │ structure("()", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## Get a GRangesList or GRanges object with mbs variants.\n", Rd_tag = "RCODE"), │ │ │ │ structure("mbs_grl <- readRDS(system.file(\"states/blood_grl_mbs.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# Count the MBSs\n", Rd_tag = "RCODE"), structure("count_mbs_contexts(mbs_grl)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/count_mbs_contexts.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# Count the MBSs\n", Rd_tag = "RCODE"), structure("count_mbs_contexts(mbs_grl)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/count_mbs_contexts.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ determine_regional_similarity (list) = structure(list(structure(list(structure("Determine regional mutation pattern similarity", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("determine_regional_similarity", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("determine_regional_similarity", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("regional_similarity", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Calculate the cosine similarities between the global mutation profile and the\n", Rd_tag = "TEXT"), │ │ │ │ @@ -664,15 +664,15 @@ │ │ │ │ structure("## We also turned verbosity on, so you can see at what step the function is.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## This can be useful on large datasets.\n", Rd_tag = "RCODE"), │ │ │ │ structure("regional_sims_0_extension = determine_regional_similarity(gr,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" ref_genome, \n", Rd_tag = "RCODE"), structure(" chromosomes,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" window_size = 40,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" stepsize = 10,\n", Rd_tag = "RCODE"), structure(" extension = 0,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" max_window_size_gen = 40000000,\n", Rd_tag = "RCODE"), │ │ │ │ - structure(" verbose = TRUE\n", Rd_tag = "RCODE"), structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/determine_regional_similarity.Rd", class = "Rd", meta = list( │ │ │ │ + structure(" verbose = TRUE\n", Rd_tag = "RCODE"), structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/determine_regional_similarity.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ enrichment_depletion_test (list) = structure(list(structure(list(structure("Test for enrichment or depletion of mutations in genomic regions", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("enrichment_depletion_test", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("enrichment_depletion_test", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function aggregates mutations per group (optional) and performs an\n", Rd_tag = "TEXT"), │ │ │ │ structure("enrichment depletion test.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -711,15 +711,15 @@ │ │ │ │ structure(" by = tissue,\n", Rd_tag = "RCODE"), structure(" p_cutoffs = 0.01, fdr_cutoffs = 0.05\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Use multiple (max 3) significance cutoffs.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## This will vary the number of significance stars.\n", Rd_tag = "RCODE"), │ │ │ │ structure("distr_multistars <- enrichment_depletion_test(distr,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" by = tissue,\n", Rd_tag = "RCODE"), structure(" p_cutoffs = c(0.05, 0.01, 0.005),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" fdr_cutoffs = c(0.1, 0.05, 0.01)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/enrichment_depletion_test.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/enrichment_depletion_test.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ extract_signatures (list) = structure(list(structure(list(structure("Extract mutational signatures from 96 mutation matrix using NMF", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("extract_signatures", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("extract_signatures", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Decomposes trinucleotide count matrix into signatures and contribution of\n", Rd_tag = "TEXT"), │ │ │ │ structure("those signatures to the spectra of the samples/vcf files.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -774,15 +774,15 @@ │ │ │ │ structure("mut_mat <- readRDS(system.file(\"states/mut_mat_data.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## This function is computationally intensive.\n", Rd_tag = "RCODE"), │ │ │ │ structure("# nmf_res <- extract_signatures(mut_mat, rank = 2)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## It's also possible to use a variational Bayes method.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## It requires the ccfindR package to work.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("# nmf_res <- extract_signatures(mut_mat, rank = 2, nmf_type = \"variational_bayes\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/extract_signatures.Rd", class = "Rd", meta = list( │ │ │ │ + structure("# nmf_res <- extract_signatures(mut_mat, rank = 2, nmf_type = \"variational_bayes\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/extract_signatures.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fit_to_signatures (list) = structure(list(structure(list(structure("Find optimal nonnegative linear combination of mutation signatures to\n", Rd_tag = "TEXT"), │ │ │ │ structure("reconstruct the mutation matrix.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fit_to_signatures", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fit_to_signatures", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Find the linear combination of mutation signatures that most closely\n", Rd_tag = "TEXT"), │ │ │ │ @@ -819,15 +819,15 @@ │ │ │ │ structure("## An example is given for indels\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Get The indel counts\n", Rd_tag = "RCODE"), │ │ │ │ structure("## See 'count_indel_contexts()' for more info on how to do this.\n", Rd_tag = "RCODE"), │ │ │ │ structure("indel_counts <- readRDS(system.file(\"states/blood_indel_counts.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Get signatures\n", Rd_tag = "RCODE"), structure("signatures <- get_known_signatures(\"indel\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE"), structure("fit_to_signatures(indel_counts, signatures)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/fit_to_signatures.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE"), structure("fit_to_signatures(indel_counts, signatures)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/fit_to_signatures.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fit_to_signatures_bootstrapped (list) = structure(list(structure(list(structure("Fit mutational signatures to a mutation matrix with bootstrapping", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fit_to_signatures_bootstrapped", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fit_to_signatures_bootstrapped", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Bootstrapping the signature refitting shows how stable the refit is, when small changes are made to the\n", Rd_tag = "TEXT"), │ │ │ │ structure("mutation matrix. You can be more confident in the refitting results, when the differences in signature\n", Rd_tag = "TEXT"), │ │ │ │ @@ -900,15 +900,15 @@ │ │ │ │ structure(" signatures,\n", Rd_tag = "RCODE"), structure(" n_boots = 2,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" max_delta = 0.004\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Use the regular refit method\n", Rd_tag = "RCODE"), │ │ │ │ structure("contri_boots <- fit_to_signatures_bootstrapped(mut_mat,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" signatures,\n", Rd_tag = "RCODE"), structure(" n_boots = 2,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" method = \"regular\"\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/fit_to_signatures_bootstrapped.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/fit_to_signatures_bootstrapped.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ fit_to_signatures_strict (list) = structure(list(structure(list(structure("Fit mutational signatures to a mutation matrix with less overfitting", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("fit_to_signatures_strict", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("fit_to_signatures_strict", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Refitting signatures with this function suffers less from overfitting.\n", Rd_tag = "TEXT"), │ │ │ │ structure("The strictness of the refitting is dependent on 'max_delta'.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -984,15 +984,15 @@ │ │ │ │ structure("## but can only be used with a limited amount of signatures.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Here we use only 5 signatures to reduce the runtime. \n", Rd_tag = "RCODE"), │ │ │ │ structure("## In practice up to 10-15 signatures could be used.\n", Rd_tag = "RCODE"), │ │ │ │ structure("best_subset_refit <- fit_to_signatures_strict(mut_mat, \n", Rd_tag = "RCODE"), │ │ │ │ structure(" signatures[,1:5], \n", Rd_tag = "RCODE"), │ │ │ │ structure(" max_delta = 0.002, \n", Rd_tag = "RCODE"), │ │ │ │ structure(" method = \"best_subset\"\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/fit_to_signatures_strict.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/fit_to_signatures_strict.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ genomic_distribution (list) = structure(list(structure(list(structure("Find overlaps between mutations and a genomic region.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("genomic_distribution", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("genomic_distribution", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Function finds the number of mutations that reside in genomic region and\n", Rd_tag = "TEXT"), │ │ │ │ structure("takes surveyed area of genome into account.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1085,15 +1085,15 @@ │ │ │ │ structure("library(rtracklayer)\n", Rd_tag = "RCODE"), │ │ │ │ structure("surveyed <- import(surveyed_file)\n", Rd_tag = "RCODE"), │ │ │ │ structure("seqlevelsStyle(surveyed) <- \"UCSC\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## For this example we use the same surveyed file for each sample.\n", Rd_tag = "RCODE"), │ │ │ │ structure("surveyed_list <- rep(list(surveyed), 9)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Calculate the number of observed and expected number of mutations in\n", Rd_tag = "RCODE"), │ │ │ │ structure("## each genomic regions for each sample.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("distr <- genomic_distribution(vcfs, surveyed_list, regions)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/genomic_distribution.Rd", class = "Rd", meta = list( │ │ │ │ + structure("distr <- genomic_distribution(vcfs, surveyed_list, regions)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/genomic_distribution.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ get_dbs_context (list) = structure(list(structure(list(structure("Get DBS context", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("get_dbs_context", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("get_dbs_context", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("DBS", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Get the DBS COSMIC context on an GRanges/GRangesList object.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1124,15 +1124,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## Get GRangesList with DBS.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## See 'get_mut_type' or 'read_vcfs_as_granges' for more info on how to do this.\n", Rd_tag = "RCODE"), │ │ │ │ structure("dbs_grl <- readRDS(system.file(\"states/blood_grl_dbs.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Set context DBS\n", Rd_tag = "RCODE"), │ │ │ │ - structure("get_dbs_context(dbs_grl)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/get_dbs_context.Rd", class = "Rd", meta = list( │ │ │ │ + structure("get_dbs_context(dbs_grl)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/get_dbs_context.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ get_indel_context (list) = structure(list(structure(list(structure("Get indel contexts", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("get_indel_context", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("get_indel_context", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Indels", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Get indel contexts\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1174,15 +1174,15 @@ │ │ │ │ structure("indel_grl <- readRDS(system.file(\"states/blood_grl_indel.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Load the corresponding reference genome.\n", Rd_tag = "RCODE"), │ │ │ │ structure("ref_genome <- \"BSgenome.Hsapiens.UCSC.hg19\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(ref_genome, character.only = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Get the indel contexts\n", Rd_tag = "RCODE"), │ │ │ │ - structure("get_indel_context(indel_grl, ref_genome)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/get_indel_context.Rd", class = "Rd", meta = list( │ │ │ │ + structure("get_indel_context(indel_grl, ref_genome)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/get_indel_context.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ get_known_signatures (list) = structure(list(structure(list(structure("Get known signatures", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("get_known_signatures", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("get_known_signatures", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function loads a signature matrix of pre-defined signatures.\n", Rd_tag = "TEXT"), │ │ │ │ structure("It can retrieve signatures for different types of mutations.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1301,15 +1301,15 @@ │ │ │ │ structure("get_known_signatures(\n", Rd_tag = "RCODE"), │ │ │ │ structure(" source = \"SIGNAL\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" sig_type = \"tissue\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" tissue_type = \"Bladder\"\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## If you use an incorrect tissue_type an error is given.\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Get sparse signatures\n", Rd_tag = "RCODE"), │ │ │ │ - structure("get_known_signatures(source = \"SPARSE\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/get_known_signatures.Rd", class = "Rd", meta = list( │ │ │ │ + structure("get_known_signatures(source = \"SPARSE\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/get_known_signatures.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ get_mut_type (list) = structure(list(structure(list(structure("Get variants with mut_type from GRanges", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("get_mut_type", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("get_mut_type", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Get the variants of a certain mutation type from a GRanges or GRangesList object.\n", Rd_tag = "TEXT"), │ │ │ │ structure("All other variants will be filtered out.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1344,15 +1344,15 @@ │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Here we only use two samples to reduce runtime\n", Rd_tag = "RCODE"), │ │ │ │ structure("grl <- grl[1:2]\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Get a specific mutation type.\n", Rd_tag = "RCODE"), │ │ │ │ structure("snv_grl <- get_mut_type(grl, \"snv\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("indel_grl <- get_mut_type(grl, \"indel\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("dbs_grl <- get_mut_type(grl, \"dbs\")\n", Rd_tag = "RCODE"), │ │ │ │ - structure("mbs_grl <- get_mut_type(grl, \"mbs\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/get_mut_type.Rd", class = "Rd", meta = list( │ │ │ │ + structure("mbs_grl <- get_mut_type(grl, \"mbs\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/get_mut_type.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ get_sim_tb (list) = structure(list(structure(list(structure("An S4 generic to get the sim_tb from a region_cossim object.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("get_sim_tb", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("get_sim_tb", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("get_sim_tb,region_cossim-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An S4 generic to get the sim_tb from a region_cossim object.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1370,15 +1370,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A tibble containing the calculated similarities of the windows.\n", Rd_tag = "TEXT"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("A tibble containing the calculated similarities of the windows.\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(list(structure("Methods (by class)", Rd_tag = "TEXT")), │ │ │ │ list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure(list(), Rd_tag = "\\item"), │ │ │ │ structure(" ", Rd_tag = "TEXT"), structure(list(structure("get_sim_tb(region_cossim)", Rd_tag = "RCODE")), Rd_tag = "\\code"), │ │ │ │ structure(": Get the sim_tb from a region_cossim object.\n", Rd_tag = "TEXT"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"))), Rd_tag = "\\section")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/get_sim_tb.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\itemize"))), Rd_tag = "\\section")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/get_sim_tb.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ hideOutput (NULL) = NULL │ │ │ │ │ │ │ │ lengthen_mut_matrix (list) = structure(list(structure(list(structure("A mutation_matrix calculated on a GRangesList or GR object modified by 'split_muts_region()',\n", Rd_tag = "TEXT"), │ │ │ │ structure("will contain a column per combination of sample and genomic region. In essence different regions\n", Rd_tag = "TEXT"), │ │ │ │ structure("are treated as different samples. This function will transform the matrix, so that these regions\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1428,15 +1428,15 @@ │ │ │ │ structure("## This also works on indels:\n", Rd_tag = "RCODE"), │ │ │ │ structure("## See the 'split_muts_region()' and 'count_indels_context()' examples for how we\n", Rd_tag = "RCODE"), │ │ │ │ structure("## obtained the indel counts:\n", Rd_tag = "RCODE"), │ │ │ │ structure("indel_counts_split <- readRDS(system.file(\"states/blood_indels_counts_split_region.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Lengthen the matrix\n", Rd_tag = "RCODE"), │ │ │ │ - structure("lengthen_mut_matrix(indel_counts_split)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/lengthen_mut_matrix.Rd", class = "Rd", meta = list( │ │ │ │ + structure("lengthen_mut_matrix(indel_counts_split)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/lengthen_mut_matrix.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ merge_signatures (list) = structure(list(structure(list(structure("Merge signatures based on cosine similarity", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("merge_signatures", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("merge_signatures", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function merges signatures based on their cosine similarity.\n", Rd_tag = "TEXT"), │ │ │ │ structure("It iteratively merges the two signatures with the highest cosine similarity.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1469,15 +1469,15 @@ │ │ │ │ structure("merge_signatures(signatures)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Merge signatures using a stricter cutoff\n", Rd_tag = "RCODE"), │ │ │ │ structure("merge_signatures(signatures, cos_sim_cutoff = 0.9)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Merge signatures using a different merging character\n", Rd_tag = "RCODE"), │ │ │ │ structure("merge_signatures(signatures, merge_char = \"_\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Merge signatures silently\n", Rd_tag = "RCODE"), │ │ │ │ - structure("merge_signatures(signatures, verbose = FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/merge_signatures.Rd", class = "Rd", meta = list( │ │ │ │ + structure("merge_signatures(signatures, verbose = FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/merge_signatures.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ mut_192_occurrences (list) = structure(list(structure(list(structure("Count 192 trinucleotide mutation occurrences", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mut_192_occurrences", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mut_192_occurrences", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("@details\n", Rd_tag = "TEXT"), │ │ │ │ structure(" This function is called by mut_matrix_stranded.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1494,15 +1494,15 @@ │ │ │ │ structure("position, for example \"U\" for untranscribed, \"T\" for transcribed strand,\n", Rd_tag = "TEXT"), │ │ │ │ structure("and \"-\" for unknown", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("gr_sizes", Rd_tag = "TEXT")), │ │ │ │ list(structure("A vector indicating the number of variants per GRanges", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Mutation matrix with 192 mutation occurrences and 96 trinucleotides\n", Rd_tag = "TEXT"), │ │ │ │ - structure("for two strands\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_192_occurrences.Rd", class = "Rd", meta = list( │ │ │ │ + structure("for two strands\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/mut_192_occurrences.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ mut_96_occurrences (list) = structure(list(structure(list(structure("Count 96 trinucleotide mutation occurrences", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mut_96_occurrences", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mut_96_occurrences", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("@details\n", Rd_tag = "TEXT"), │ │ │ │ structure(" This function is called by mut_matrix. It calculates the 96 trinucleotide context for all variants\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1511,15 +1511,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("type_context", Rd_tag = "TEXT")), list( │ │ │ │ structure("result from type_context function", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure("gr_sizes", Rd_tag = "TEXT")), │ │ │ │ list(structure("A vector indicating the number of variants per GRanges", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ - structure(list(structure("\n", Rd_tag = "TEXT"), structure("Mutation matrix with 96 trinucleotide mutation occurrences\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_96_occurrences.Rd", class = "Rd", meta = list( │ │ │ │ + structure(list(structure("\n", Rd_tag = "TEXT"), structure("Mutation matrix with 96 trinucleotide mutation occurrences\n", Rd_tag = "TEXT")), Rd_tag = "\\value")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/mut_96_occurrences.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ mut_context (list) = structure(list(structure(list(structure("Retrieve context of base substitutions", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mut_context", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mut_context", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A function to extract the bases 3' upstream and 5' downstream of the base\n", Rd_tag = "TEXT"), │ │ │ │ structure("substitutions from the reference genome. The user an choose how many bases\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1546,15 +1546,15 @@ │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Load the corresponding reference genome.\n", Rd_tag = "RCODE"), │ │ │ │ structure("ref_genome <- \"BSgenome.Hsapiens.UCSC.hg19\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(ref_genome, character.only = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Get the standard context\n", Rd_tag = "RCODE"), │ │ │ │ structure("mut_context <- mut_context(vcfs[[1]], ref_genome)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Get larger context\n", Rd_tag = "RCODE"), │ │ │ │ - structure("mut_context_larger <- mut_context(vcfs[[1]], ref_genome, extension = 2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_context.Rd", class = "Rd", meta = list( │ │ │ │ + structure("mut_context_larger <- mut_context(vcfs[[1]], ref_genome, extension = 2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/mut_context.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ mut_matrix (list) = structure(list(structure(list(structure("Make mutation count matrix of 96 trinucleotides", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mut_matrix", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mut_matrix", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Make 96 trinucleotide mutation count matrix\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mut_matrix(vcf_list, ref_genome, extension = 1)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1580,15 +1580,15 @@ │ │ │ │ structure("## Load the corresponding reference genome.\n", Rd_tag = "RCODE"), │ │ │ │ structure("ref_genome <- \"BSgenome.Hsapiens.UCSC.hg19\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(ref_genome, character.only = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Construct a mutation matrix from the loaded VCFs in comparison to the\n", Rd_tag = "RCODE"), │ │ │ │ structure("## ref_genome.\n", Rd_tag = "RCODE"), structure("mut_mat <- mut_matrix(vcf_list = grl, ref_genome = ref_genome)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Construct a mutation matrix with a larger context.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## This is most usefull when you have many mutations per sample.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("mut_mat_extended <- mut_matrix(vcf_list = grl, ref_genome = ref_genome, extension = 2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_matrix.Rd", class = "Rd", meta = list( │ │ │ │ + structure("mut_mat_extended <- mut_matrix(vcf_list = grl, ref_genome = ref_genome, extension = 2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/mut_matrix.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ mut_matrix_stranded (list) = structure(list(structure(list(structure("Make mutation count matrix of 96 trinucleotides with\n", Rd_tag = "TEXT"), │ │ │ │ structure("strand information", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mut_matrix_stranded", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mut_matrix_stranded", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Make a mutation count matrix with 192 features: 96 trinucleotides and 2 strands,\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1662,15 +1662,15 @@ │ │ │ │ structure("# You can specify your preferred order of the levels:\n", Rd_tag = "RCODE"), │ │ │ │ structure("repli_strand_granges$strand_info <- factor(\n", Rd_tag = "RCODE"), │ │ │ │ structure(" repli_strand_granges$strand_info,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" levels = c(\"left\", \"right\")\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("mut_mat_s_rep <- mut_matrix_stranded(grl, ref_genome, repli_strand_granges,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" mode = \"replication\"\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_matrix_stranded.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/mut_matrix_stranded.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ mut_strand (list) = structure(list(structure(list(structure("Find strand of mutations", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mut_strand", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mut_strand", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Find strand of mutations\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mut_strand(vcf, ranges, mode = \"transcription\")\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1739,15 +1739,15 @@ │ │ │ │ structure(" ranges = IRanges(\n", Rd_tag = "RCODE"), │ │ │ │ structure(" start = repli_strand$Start + 1,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" end = repli_strand$Stop\n", Rd_tag = "RCODE"), │ │ │ │ structure(" ),\n", Rd_tag = "RCODE"), structure(" strand_info = repli_strand$Class\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("## UCSC seqlevelsstyle\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(GenomeInfoDb)\n", Rd_tag = "RCODE"), │ │ │ │ structure("seqlevelsStyle(repli_strand_granges) <- \"UCSC\"\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE"), structure("mut_strand(vcfs[[1]], repli_strand_granges, mode = \"transcription\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_strand.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE"), structure("mut_strand(vcfs[[1]], repli_strand_granges, mode = \"transcription\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/mut_strand.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ mut_type (list) = structure(list(structure(list(structure("Retrieve base substitution types from a VCF object", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mut_type", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mut_type", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A function to extract the base substitutions from a vcf and translate to\n", Rd_tag = "TEXT"), │ │ │ │ structure("the 6 common base substitution types.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -1760,15 +1760,15 @@ │ │ │ │ structure(list(structure("read_vcfs_as_granges", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## See the 'read_vcfs_as_granges()' example for how we obtained the\n", Rd_tag = "RCODE"), │ │ │ │ structure("## following data:\n", Rd_tag = "RCODE"), │ │ │ │ structure("vcfs <- readRDS(system.file(\"states/read_vcfs_as_granges_output.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ - structure("mut_type(vcfs[[1]])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_type.Rd", class = "Rd", meta = list( │ │ │ │ + structure("mut_type(vcfs[[1]])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/mut_type.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ mut_type_occurrences (list) = structure(list(structure(list(structure("Count the occurrences of each base substitution type", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mut_type_occurrences", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mut_type_occurrences", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Count the occurrences of each base substitution type\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mut_type_occurrences(vcf_list, ref_genome)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1788,15 +1788,15 @@ │ │ │ │ structure("vcfs <- readRDS(system.file(\"states/read_vcfs_as_granges_output.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Load a reference genome.\n", Rd_tag = "RCODE"), │ │ │ │ structure("ref_genome <- \"BSgenome.Hsapiens.UCSC.hg19\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(ref_genome, character.only = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Get the type occurrences for all VCF objects.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("type_occurrences <- mut_type_occurrences(vcfs, ref_genome)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_type_occurrences.Rd", class = "Rd", meta = list( │ │ │ │ + structure("type_occurrences <- mut_type_occurrences(vcfs, ref_genome)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/mut_type_occurrences.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ mutations_from_vcf (list) = structure(list(structure(list(structure("Retrieve base substitutions from vcf", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("mutations_from_vcf", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("mutations_from_vcf", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A function to extract base substitutions of each position in vcf\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("mutations_from_vcf(vcf)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1808,15 +1808,15 @@ │ │ │ │ structure(list(structure("read_vcfs_as_granges", Rd_tag = "TEXT")), Rd_tag = "\\link")), Rd_tag = "\\code"), │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## See the 'read_vcfs_as_granges()' example for how we obtained the\n", Rd_tag = "RCODE"), │ │ │ │ structure("## following data:\n", Rd_tag = "RCODE"), │ │ │ │ structure("vcfs <- readRDS(system.file(\"states/read_vcfs_as_granges_output.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ - structure("muts <- mutations_from_vcf(vcfs[[1]])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mutations_from_vcf.Rd", class = "Rd", meta = list( │ │ │ │ + structure("muts <- mutations_from_vcf(vcfs[[1]])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/mutations_from_vcf.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_192_profile (list) = structure(list(structure(list(structure("Plot 192 trinucleotide profile", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_192_profile", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_192_profile", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot relative contribution of 192 trinucleotides\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("plot_192_profile(mut_matrix, colors = NA, ymax = 0.2, condensed = FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1855,15 +1855,15 @@ │ │ │ │ structure("## See 'extract_signatures()' on how we obtained these signatures.\n", Rd_tag = "RCODE"), │ │ │ │ structure("nmf_res_strand <- readRDS(system.file(\"states/nmf_res_strand_data.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Optionally, provide signature names\n", Rd_tag = "RCODE"), │ │ │ │ structure("colnames(nmf_res_strand$signatures) <- c(\"Signature A\", \"Signature B\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Generate the plot\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_192_profile(nmf_res_strand$signatures)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_192_profile.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_192_profile(nmf_res_strand$signatures)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_192_profile.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_96_profile (list) = structure(list(structure(list(structure("Plot 96 trinucleotide profile", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_96_profile", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_96_profile", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot relative contribution of 96 trinucleotides\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("plot_96_profile(mut_matrix, colors = NA, ymax = 0.2, condensed = FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -1902,15 +1902,15 @@ │ │ │ │ structure("## See 'extract_signatures()' on how we obtained these signatures.\n", Rd_tag = "RCODE"), │ │ │ │ structure("nmf_res <- readRDS(system.file(\"states/nmf_res_data.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Optionally, provide signature names\n", Rd_tag = "RCODE"), │ │ │ │ structure("colnames(nmf_res$signatures) <- c(\"Signature A\", \"Signature B\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Generate the plot\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_96_profile(nmf_res$signatures)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_96_profile.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_96_profile(nmf_res$signatures)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_96_profile.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_bootstrapped_contribution (list) = structure(list(structure(list(structure("Plot the bootstrapped signature contributions", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_bootstrapped_contribution", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_bootstrapped_contribution", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot the signature contributions retrieved with 'fit_to_signatures_bootstrapped'.\n", Rd_tag = "TEXT"), │ │ │ │ structure("The function can plot both the absolute or the relative signature contribution.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -1939,15 +1939,15 @@ │ │ │ │ structure("## Plot bootstrapped contribution\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_bootstrapped_contribution(contri_boots)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Plot bootstrapped contribution with relative contributions\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_bootstrapped_contribution(contri_boots, mode = \"relative\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Plot bootstrapped contribution with a barplot\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_bootstrapped_contribution(contri_boots, plot_type = \"barplot\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Plot bootstrapped contribution with a dotplot\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_bootstrapped_contribution(contri_boots, plot_type = \"dotplot\", mode = \"absolute\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_bootstrapped_contribution.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_bootstrapped_contribution(contri_boots, plot_type = \"dotplot\", mode = \"absolute\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_bootstrapped_contribution.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_compare_dbs (list) = structure(list(structure(list(structure("Compare two DBS mutation profiles", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_compare_dbs", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_compare_dbs", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("DBS", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plots two DBS mutation profiles and their difference, reports the residual\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2023,15 +2023,15 @@ │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## You can also change the y limits.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## This can be done separately for the profiles and the different facets.\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_compare_dbs(dbs_counts[, 1],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" dbs_counts[, 2],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" profile_ymax = 0.3,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" diff_ylim = c(-0.03, 0.03)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_compare_dbs.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_compare_dbs.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_compare_indels (list) = structure(list(structure(list(structure("Compare two indel mutation profiles", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_compare_indels", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_compare_indels", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Indels", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plots two indel mutation profiles and their difference, reports the residual\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2109,15 +2109,15 @@ │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## You can also change the y limits.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## This can be done separately for the profiles and the different facets.\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_compare_indels(indel_counts[, 1],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" indel_counts[, 2],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" profile_ymax = 0.3,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" diff_ylim = c(-0.03, 0.03)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_compare_indels.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_compare_indels.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_compare_mbs (list) = structure(list(structure(list(structure("Compare two mbs mutation profiles", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_compare_mbs", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_compare_mbs", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("MBS", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plots two mbs mutation profiles and their difference, reports the residual\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2182,15 +2182,15 @@ │ │ │ │ structure("plot_compare_mbs(mbs_counts[, 1],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" mbs_counts[, 2],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" profile_ymax = 0.9,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" diff_ylim = c(-0.8, 0.8)\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## You could also compare a reconstructed profile.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## However, the example data does not contain enough MBS variants to use NMF.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("## Existing signatures have also not yet been defined.\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_compare_mbs.Rd", class = "Rd", meta = list( │ │ │ │ + structure("## Existing signatures have also not yet been defined.\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_compare_mbs.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_compare_profiles (list) = structure(list(structure(list(structure("Compare two 96 mutation profiles", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_compare_profiles", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_compare_profiles", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plots two 96 mutation profiles and their difference, reports the residual\n", Rd_tag = "TEXT"), │ │ │ │ structure("sum of squares (RSS).\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2261,15 +2261,15 @@ │ │ │ │ structure(" mut_mat[, 1],\n", Rd_tag = "RCODE"), structure(" mut_mat[, 2]\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## You can also change the y limits.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## This can be done separately for the profiles and the different facets.\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_compare_profiles(mut_mat[, 1],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" mut_mat[, 2],\n", Rd_tag = "RCODE"), structure(" profile_ymax = 0.3,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" diff_ylim = c(-0.03, 0.03)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_compare_profiles.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_compare_profiles.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_contribution (list) = structure(list(structure(list(structure("Plot signature contribution barplot", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_contribution", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_contribution", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot contribution of signatures. Can be used on both the results of a NMF\n", Rd_tag = "TEXT"), │ │ │ │ structure("and on the results of signature refitting.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2341,15 +2341,15 @@ │ │ │ │ structure("## Here we load some data as an example\n", Rd_tag = "RCODE"), │ │ │ │ structure("fit_res <- readRDS(system.file(\"states/snv_refit.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("plot_contribution(fit_res$contribution)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Or again in absolute mode\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_contribution(fit_res$contribution,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" mode = \"absolute\"\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_contribution.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_contribution.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_contribution_heatmap (list) = structure(list(structure(list(structure("Plot signature contribution heatmap", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_contribution_heatmap", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_contribution_heatmap", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot relative contribution of signatures in a heatmap\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("plot_contribution_heatmap(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -2416,15 +2416,15 @@ │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## It's also possible to create a contribution heatmap with text values\n", Rd_tag = "RCODE"), │ │ │ │ structure("output_text <- plot_contribution_heatmap(nmf_res$contribution, plot_values = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## This function can also be used on the result of a signature refitting analysis.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Here we load a existing result as an example.\n", Rd_tag = "RCODE"), │ │ │ │ structure("snv_refit <- readRDS(system.file(\"states/strict_snv_refit.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ - structure("))\n", Rd_tag = "RCODE"), structure("plot_contribution_heatmap(snv_refit$contribution, cluster_samples = TRUE, cluster_sigs = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_contribution_heatmap.Rd", class = "Rd", meta = list( │ │ │ │ + structure("))\n", Rd_tag = "RCODE"), structure("plot_contribution_heatmap(snv_refit$contribution, cluster_samples = TRUE, cluster_sigs = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_contribution_heatmap.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_correlation_bootstrap (list) = structure(list(structure(list(structure("Plots the correlation between bootstrapped signature contributions", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_correlation_bootstrap", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_correlation_bootstrap", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function plots the pearson correlation between signatures.\n", Rd_tag = "TEXT"), │ │ │ │ structure("This can be done per sample or for all samples together.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2446,15 +2446,15 @@ │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Plot the correlations between signatures per sample\n", Rd_tag = "RCODE"), │ │ │ │ structure("fig_l <- plot_correlation_bootstrap(contri_boots)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Look at the figure of the first sample.\n", Rd_tag = "RCODE"), │ │ │ │ structure("fig_l[[1]]\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## You can also look at the correlation for all samples combined\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_correlation_bootstrap(contri_boots, per_sample = FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_correlation_bootstrap.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_correlation_bootstrap(contri_boots, per_sample = FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_correlation_bootstrap.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_cosine_heatmap (list) = structure(list(structure(list(structure("Plot cosine similarity heatmap", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_cosine_heatmap", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_cosine_heatmap", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot pairwise cosine similarities in a heatmap.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("plot_cosine_heatmap(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -2523,15 +2523,15 @@ │ │ │ │ structure(" row_order = sample_order, col_order = cosmic_order\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## You can also plot the similarity of samples with eachother\n", Rd_tag = "RCODE"), │ │ │ │ structure("cos_matrix <- cos_sim_matrix(mut_mat, mut_mat)\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_cosine_heatmap(cos_matrix, cluster_rows = TRUE, cluster_cols = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## It's also possible to add the actual values in the heatmap.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_cosine_heatmap(cos_matrix, cluster_rows = TRUE, cluster_cols = TRUE, plot_values = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_cosine_heatmap.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_cosine_heatmap(cos_matrix, cluster_rows = TRUE, cluster_cols = TRUE, plot_values = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_cosine_heatmap.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_dbs_contexts (list) = structure(list(structure(list(structure("Plot the DBS contexts", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_dbs_contexts", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_dbs_contexts", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("DBS", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot the DBS contexts\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2573,15 +2573,15 @@ │ │ │ │ structure("dbs_counts <- readRDS(system.file(\"states/blood_dbs_counts.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Plot contexts\n", Rd_tag = "RCODE"), structure("plot_dbs_contexts(dbs_counts)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Use the same y axis for all samples.\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_dbs_contexts(dbs_counts, same_y = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Create a more condensed plot\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_dbs_contexts(dbs_counts, condensed = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_dbs_contexts.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_dbs_contexts(dbs_counts, condensed = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_dbs_contexts.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_enrichment_depletion (list) = structure(list(structure(list(structure("Plot enrichment/depletion of mutations in genomic regions", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_enrichment_depletion", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_enrichment_depletion", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot enrichment/depletion of mutations in genomic regions\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("plot_enrichment_depletion(df, sig_type = c(\"fdr\", \"p\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -2621,15 +2621,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Plot with p values instead of fdr\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_enrichment_depletion(distr_test, sig_type = \"p\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Use multiple (max 3) significance cutoffs.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## This will vary the number of significance stars.\n", Rd_tag = "RCODE"), │ │ │ │ structure("distr_multistars <- enrichment_depletion_test(distr,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" by = tissue,\n", Rd_tag = "RCODE"), structure(" p_cutoffs = c(0.05, 0.01, 0.005),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" fdr_cutoffs = c(0.1, 0.05, 0.01)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE"), structure("plot_enrichment_depletion(distr_multistars)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_enrichment_depletion.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE"), structure("plot_enrichment_depletion(distr_multistars)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_enrichment_depletion.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_indel_contexts (list) = structure(list(structure(list(structure("Plot the indel contexts", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_indel_contexts", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_indel_contexts", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Indels", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot the indel contexts\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2687,15 +2687,15 @@ │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Plot contexts\n", Rd_tag = "RCODE"), structure("plot_indel_contexts(indel_counts)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Use the same y axis for all samples.\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_indel_contexts(indel_counts, same_y = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Add extra labels to make plot clearer\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_indel_contexts(indel_counts, extra_labels = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Create a more condensed plot\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_indel_contexts(indel_counts, condensed = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_indel_contexts.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_indel_contexts(indel_counts, condensed = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_indel_contexts.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_lesion_segregation (list) = structure(list(structure(list(structure("Plot the strands of variants to show lesion segregation", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_lesion_segregation", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_lesion_segregation", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Lesion_segregation", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The strands of variants in a GRanges object is plotted.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -2759,15 +2759,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Plot lesion segregation per chromosome.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## We here store the results in a list.\n", Rd_tag = "RCODE"), │ │ │ │ structure("figure_l = plot_lesion_segregation(gr, per_chrom = TRUE, sample_name = \"Colon1\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Plot specific chromosomes in a user specified order\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_lesion_segregation(grl[1:3], chromosomes = c(2,3))\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Subsample the mutations, so less points are plotted.\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_lesion_segregation(grl[1:3], subsample = 0.2)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_lesion_segregation.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_lesion_segregation.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_main_dbs_contexts (list) = structure(list(structure(list(structure("Plot the main DBS contexts", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_main_dbs_contexts", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_main_dbs_contexts", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("DBS", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot the main DBS contexts\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2805,15 +2805,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## Get The DBS counts\n", Rd_tag = "RCODE"), │ │ │ │ structure("## See 'count_dbs_contexts()' for more info on how to do this.\n", Rd_tag = "RCODE"), │ │ │ │ structure("dbs_counts <- readRDS(system.file(\"states/blood_dbs_counts.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Plot contexts\n", Rd_tag = "RCODE"), structure("plot_main_dbs_contexts(dbs_counts)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Use the same y axis for all samples.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_main_dbs_contexts(dbs_counts, same_y = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_main_dbs_contexts.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_main_dbs_contexts(dbs_counts, same_y = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_main_dbs_contexts.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_main_indel_contexts (list) = structure(list(structure(list(structure("Plot the main indel contexts", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_main_indel_contexts", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_main_indel_contexts", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("Indels", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot the main indel contexts\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2851,15 +2851,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## Get The indel counts\n", Rd_tag = "RCODE"), │ │ │ │ structure("## See 'count_indel_contexts()' for more info on how to do this.\n", Rd_tag = "RCODE"), │ │ │ │ structure("indel_counts <- readRDS(system.file(\"states/blood_indel_counts.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Plot contexts\n", Rd_tag = "RCODE"), structure("plot_main_indel_contexts(indel_counts)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Use the same y axis for all samples.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_main_indel_contexts(indel_counts, same_y = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_main_indel_contexts.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_main_indel_contexts(indel_counts, same_y = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_main_indel_contexts.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_mbs_contexts (list) = structure(list(structure(list(structure("Plot the MBS contexts", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_mbs_contexts", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_mbs_contexts", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("MBS", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot the MBS contexts\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2888,15 +2888,15 @@ │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## Get The mbs counts\n", Rd_tag = "RCODE"), │ │ │ │ structure("## See 'count_mbs_contexts()' for more info on how to do this.\n", Rd_tag = "RCODE"), │ │ │ │ structure("mbs_counts <- readRDS(system.file(\"states/blood_mbs_counts.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Plot contexts\n", Rd_tag = "RCODE"), structure("plot_mbs_contexts(mbs_counts)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Use a different y axis for all samples.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_mbs_contexts(mbs_counts, same_y = FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_mbs_contexts.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_mbs_contexts(mbs_counts, same_y = FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_mbs_contexts.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_original_vs_reconstructed (list) = structure(list(structure(list(structure("Plot the similarity between a mutation matrix and its reconstructed profile", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_original_vs_reconstructed", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_original_vs_reconstructed", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("When a reconstructed profile has a cosine similarity of more than 0.95 with\n", Rd_tag = "TEXT"), │ │ │ │ structure("original, the reconstructed profile is considered very good.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2936,15 +2936,15 @@ │ │ │ │ structure("## Here we load some data as an example\n", Rd_tag = "RCODE"), │ │ │ │ structure("fit_res <- readRDS(system.file(\"states/snv_refit.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("plot_original_vs_reconstructed(mut_mat, fit_res$reconstructed)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## You can also change the height of the horizontal line\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_original_vs_reconstructed(mut_mat, fit_res$reconstructed, y_intercept = 0.90)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## It's also possible to change the limits of the y axis\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_original_vs_reconstructed(mut_mat, fit_res$reconstructed, ylims = c(0, 1))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_original_vs_reconstructed.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_original_vs_reconstructed(mut_mat, fit_res$reconstructed, ylims = c(0, 1))\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_original_vs_reconstructed.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_profile_heatmap (list) = structure(list(structure(list(structure("Plot a mutation matrix as a heatmap", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_profile_heatmap", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_profile_heatmap", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Function to plot a SNV mutation matrix as a heatmap.\n", Rd_tag = "TEXT"), │ │ │ │ structure("This is especially useful when looking at a wide mutational context.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -2994,15 +2994,15 @@ │ │ │ │ structure("plot_profile_heatmap(mut_mat_extended, by = tissue)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Or plot the heatmap per sample.\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_profile_heatmap(mut_mat_extended,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" by = colnames(mut_mat_extended),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" max = 0.05\n", Rd_tag = "RCODE"), structure(")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Create a condensed heatmap of extended profile\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_profile_heatmap(mut_mat_extended, condensed = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_profile_heatmap.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_profile_heatmap(mut_mat_extended, condensed = TRUE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_profile_heatmap.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_profile_region (list) = structure(list(structure(list(structure("Plot 96 trinucleotide profile per subgroup", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_profile_region", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_profile_region", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("genomic_regions", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot relative contribution of 96 trinucleotides per subgroup.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3053,15 +3053,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\seealso"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## See the 'lengthen_mut_matrix()' example for how we obtained the\n", Rd_tag = "RCODE"), │ │ │ │ structure("## mutation matrix information:\n", Rd_tag = "RCODE"), │ │ │ │ structure("mut_mat_long <- readRDS(system.file(\"states/mut_mat_longregions.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Plot the 96-profile of three samples\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_profile_region(mut_mat_long[, c(1, 4, 7)])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_profile_region.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_profile_region(mut_mat_long[, c(1, 4, 7)])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_profile_region.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_rainfall (list) = structure(list(structure(list(structure("Plot genomic rainfall", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_rainfall", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_rainfall", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Rainfall plot visualizes the types of mutations and intermutation distance\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("plot_rainfall(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -3132,15 +3132,15 @@ │ │ │ │ structure("## See 'indel_get_context' for more info on how to do this.\n", Rd_tag = "RCODE"), │ │ │ │ structure("grl_indel_context <- readRDS(system.file(\"states/blood_grl_indel_context.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_rainfall(grl_indel_context[[1]],\n", Rd_tag = "RCODE"), │ │ │ │ structure(" title = \"Indel rainfall\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" chromosomes,\n", Rd_tag = "RCODE"), structure(" type = \"indel\"\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_rainfall.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_rainfall.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_regional_similarity (list) = structure(list(structure(list(structure("Plot regional similarity", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_regional_similarity", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_regional_similarity", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("regional_similarity", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot the cosine similarity of the mutation profiles of small genomic windows\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3213,15 +3213,15 @@ │ │ │ │ structure("fig_l = plot_regional_similarity(regional_sims, per_chrom = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Plot without a title\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_regional_similarity(regional_sims, title = \"\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Add a rug to the plot, that shows the location of the mutations.\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_regional_similarity(regional_sims, plot_rug = FALSE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Use custom x axis breaks\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_regional_similarity(regional_sims, x_axis_breaks = c(50, 150))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_regional_similarity.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_regional_similarity.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_river (list) = structure(list(structure(list(structure("Plot a riverplot", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_river", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_river", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Function to plot a SNV mutation matrix as a riverplot.\n", Rd_tag = "TEXT"), │ │ │ │ structure("This is especially useful when looking at a wide\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3255,15 +3255,15 @@ │ │ │ │ structure("mut_mat_extended <- readRDS(system.file(\"states/mut_mat_data_extended.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Create heatmap of extended profile\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_river(mut_mat_extended[,c(1,4)])\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Create condensed version of riverplot\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_river(mut_mat_extended[,c(1,4)], condensed = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ - structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_river.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_river.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_signature_strand_bias (list) = structure(list(structure(list(structure("Plot signature strand bias", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_signature_strand_bias", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_signature_strand_bias", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot strand bias per mutation type for each signature.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("plot_signature_strand_bias(signatures_strand_bias)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -3288,15 +3288,15 @@ │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Provide column names for the plot.\n", Rd_tag = "RCODE"), │ │ │ │ structure("colnames(nmf_res_strand$signatures) <- c(\"Signature A\", \"Signature B\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Creat figure\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_signature_strand_bias(nmf_res_strand$signatures)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## You can also plot the bias of samples\n", Rd_tag = "RCODE"), │ │ │ │ - structure("plot_signature_strand_bias(mut_mat_s[, c(1, 2)])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_signature_strand_bias.Rd", class = "Rd", meta = list( │ │ │ │ + structure("plot_signature_strand_bias(mut_mat_s[, c(1, 2)])\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_signature_strand_bias.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_spectrum (list) = structure(list(structure(list(structure("Plot point mutation spectrum", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_spectrum", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_spectrum", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot point mutation spectrum\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("plot_spectrum(\n", Rd_tag = "RCODE"), │ │ │ │ @@ -3380,15 +3380,15 @@ │ │ │ │ structure("my_colors <- c(\n", Rd_tag = "RCODE"), structure(" \"pink\", \"orange\", \"blue\", \"lightblue\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \"green\", \"red\", \"purple\"\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## And use them in a plot.\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_spectrum(type_occurrences,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" CT = TRUE,\n", Rd_tag = "RCODE"), structure(" legend = TRUE,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" colors = my_colors\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_spectrum.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_spectrum.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_spectrum_region (list) = structure(list(structure(list(structure("Plot point mutation spectrum per genomic region", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_spectrum_region", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_spectrum_region", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("genomic_regions", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A spectrum similar to the one from 'plot_spectrum()' is plotted.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3511,15 +3511,15 @@ │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_spectrum_region(type_occurrences, by = sample_names, error_bars = \"none\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Plot it in a more condensed manner, \n", Rd_tag = "RCODE"), │ │ │ │ structure("## which is is ideal for publications.\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_spectrum_region(type_occurrences, \n", Rd_tag = "RCODE"), │ │ │ │ structure("by = sample_names, \n", Rd_tag = "RCODE"), │ │ │ │ structure("error_bars = \"none\", \n", Rd_tag = "RCODE"), │ │ │ │ - structure("condensed = TRUE)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_spectrum_region.Rd", class = "Rd", meta = list( │ │ │ │ + structure("condensed = TRUE)\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_spectrum_region.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_strand (list) = structure(list(structure(list(structure("Plot strand per base substitution type", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_strand", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_strand", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("For each base substitution type and transcriptional strand the total number\n", Rd_tag = "TEXT"), │ │ │ │ structure("of mutations and the relative contribution within a group is returned.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -3556,15 +3556,15 @@ │ │ │ │ structure(" \"intestine\", \"intestine\", \"intestine\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \"liver\", \"liver\", \"liver\"\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("strand_counts <- strand_occurrences(mut_mat_s, by = tissue)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Plot the strand in relative mode.\n", Rd_tag = "RCODE"), │ │ │ │ structure("strand_plot <- plot_strand(strand_counts)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Or absolute mode.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("strand_plot <- plot_strand(strand_counts, mode = \"absolute\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_strand.Rd", class = "Rd", meta = list( │ │ │ │ + structure("strand_plot <- plot_strand(strand_counts, mode = \"absolute\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_strand.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ plot_strand_bias (list) = structure(list(structure(list(structure("Plot strand bias per base substitution type per group", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("plot_strand_bias", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("plot_strand_bias", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Plot strand bias per base substitution type per group\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("plot_strand_bias(strand_bias, colors = NA, sig_type = c(\"fdr\", \"p\"))\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -3607,15 +3607,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Plot the strand bias.\n", Rd_tag = "RCODE"), │ │ │ │ structure("plot_strand_bias(strand_bias)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Use multiple (max 3) significance cutoffs.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## This will vary the number of significance stars.\n", Rd_tag = "RCODE"), │ │ │ │ structure("strand_bias_multistars <- strand_bias_test(strand_counts,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" p_cutoffs = c(0.05, 0.01, 0.005),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" fdr_cutoffs = c(0.1, 0.05, 0.01)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE"), structure("plot_strand_bias(strand_bias_multistars)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_strand_bias.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE"), structure("plot_strand_bias(strand_bias_multistars)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/plot_strand_bias.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ pool_mut_mat (list) = structure(list(structure(list(structure("Pool multiple samples from a mutation matrix together", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("pool_mut_mat", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("pool_mut_mat", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The mutation counts of columns (samples) are added up according to the grouping variable.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("pool_mut_mat(mut_matrix, grouping)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ @@ -3629,15 +3629,15 @@ │ │ │ │ structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("Mutation count matrix (dimensions: x mutation types\n", Rd_tag = "TEXT"), │ │ │ │ structure("X n groups)\n", Rd_tag = "TEXT")), Rd_tag = "\\value"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure("## See the 'mut_matrix()' example for how we obtained the mutation matrix:\n", Rd_tag = "RCODE"), │ │ │ │ structure("mut_mat <- readRDS(system.file(\"states/mut_mat_data.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("grouping <- c(rep(\"colon\", 3), rep(\"intestine\", 3), rep(\"liver\", 3))\n", Rd_tag = "RCODE"), │ │ │ │ - structure("pool_mut_mat(mut_mat, grouping)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/pool_mut_mat.Rd", class = "Rd", meta = list( │ │ │ │ + structure("pool_mut_mat(mut_mat, grouping)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/pool_mut_mat.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ read_vcfs_as_granges (list) = structure(list(structure(list(structure("Read VCF files into a GRangesList", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("read_vcfs_as_granges", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("read_vcfs_as_granges", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function reads Variant Call Format (VCF) files into a GRanges object\n", Rd_tag = "TEXT"), │ │ │ │ structure("and combines them in a GRangesList. In addition to loading the files, this\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3728,15 +3728,15 @@ │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Loading only indels can be done like this.\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Select data containing indels.\n", Rd_tag = "RCODE"), │ │ │ │ structure("vcf_fnames <- list.files(system.file(\"extdata\", package = \"MutationalPatterns\"),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" pattern = \"blood.*vcf\", full.names = TRUE\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("sample_names <- c(\"AC\", \"ACC55\", \"BCH\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Read data and select only the indels.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Other mutation types can be read in the same way.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("read_vcfs_as_granges(vcf_fnames, sample_names, ref_genome, type = \"indel\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/read_vcfs_as_granges.Rd", class = "Rd", meta = list( │ │ │ │ + structure("read_vcfs_as_granges(vcf_fnames, sample_names, ref_genome, type = \"indel\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/read_vcfs_as_granges.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ region_cossim-class (list) = structure(list(structure(list(structure("An S4 class to store the results of a regional mutation pattern similarity\n", Rd_tag = "TEXT"), │ │ │ │ structure("analysis", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("region_cossim-class", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("region_cossim-class", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An S4 class to store the results of a regional mutation pattern similarity\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3778,15 +3778,15 @@ │ │ │ │ structure(list(list(structure(list(structure("chromosomes", Rd_tag = "RCODE")), Rd_tag = "\\code")), │ │ │ │ list(structure("Vector of chromosome/contig names of the reference genome\n", Rd_tag = "TEXT"), │ │ │ │ structure("to be plotted.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ structure("\n", Rd_tag = "TEXT"), structure("\n", Rd_tag = "TEXT"), │ │ │ │ structure(list(list(structure(list(structure("exclude_self_mut_mat", Rd_tag = "RCODE")), Rd_tag = "\\code")), │ │ │ │ list(structure("Boolean describing whether the mutations in a\n", Rd_tag = "TEXT"), │ │ │ │ structure("window should be subtracted from the global mutation matrix.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\describe"))), Rd_tag = "\\section")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/region_cossim-class.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\describe"))), Rd_tag = "\\section")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/region_cossim-class.Rd", class = "Rd", meta = list( │ │ │ │ docType = "class", generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ rename_nmf_signatures (list) = structure(list(structure(list(structure("Rename NMF signatures based on previously defined signatures", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("rename_nmf_signatures", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("rename_nmf_signatures", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function renames signatures identified with NMF based on previously defined signatures.\n", Rd_tag = "TEXT"), │ │ │ │ structure("If a NMF signature has a cosine similarity with a previously defined signature,\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3830,15 +3830,15 @@ │ │ │ │ structure("## Get signatures\n", Rd_tag = "RCODE"), structure("signatures <- get_known_signatures()\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("rename_nmf_signatures(nmf_res, signatures)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## You can change or remove the suffix of the renamed signatures.\n", Rd_tag = "RCODE"), │ │ │ │ structure("rename_nmf_signatures(nmf_res, signatures, suffix = \"\")\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## You can change how similar the signatures have to be, before they are considered similar.\n", Rd_tag = "RCODE"), │ │ │ │ structure("rename_nmf_signatures(nmf_res, signatures, cutoff = 0.95)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## You can also change the base_name of the signatures that end up with a letter name.\n", Rd_tag = "RCODE"), │ │ │ │ - structure("rename_nmf_signatures(nmf_res, signatures, cutoff = 0.95, base_name = \"Signature_\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/rename_nmf_signatures.Rd", class = "Rd", meta = list( │ │ │ │ + structure("rename_nmf_signatures(nmf_res, signatures, cutoff = 0.95, base_name = \"Signature_\")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/rename_nmf_signatures.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ safeDeparse (closure) = function (obj) │ │ │ │ { │ │ │ │ tryCatch({ │ │ │ │ deparse(obj) │ │ │ │ }, error = function(e) { │ │ │ │ @@ -3851,15 +3851,15 @@ │ │ │ │ structure(list(structure("show,region_cossim-method", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("An S4 method to show an instance of the region_cossim class.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ structure(list(structure("\n", Rd_tag = "RCODE"), structure(list( │ │ │ │ list(structure("show", Rd_tag = "TEXT")), list(structure("region_cossim", Rd_tag = "TEXT"))), Rd_tag = "\\S4method"), │ │ │ │ structure("(object)\n", Rd_tag = "RCODE")), Rd_tag = "\\usage"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure(list( │ │ │ │ list(structure("object", Rd_tag = "TEXT")), list(structure("A region_cossim object.", Rd_tag = "TEXT"))), Rd_tag = "\\item"), │ │ │ │ - structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/show-region_cossim-method.Rd", class = "Rd", meta = list( │ │ │ │ + structure("\n", Rd_tag = "TEXT")), Rd_tag = "\\arguments")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/show-region_cossim-method.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ signature_potential_damage_analysis (list) = structure(list(structure(list(structure("Potential damage analysis for the supplied mutational signatures", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("signature_potential_damage_analysis", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("signature_potential_damage_analysis", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("The ratio of possible 'stop gain', 'mismatches', 'synonymous mutations' and\n", Rd_tag = "TEXT"), │ │ │ │ structure("'splice site mutations' is counted per signature. Normalized ratios are also\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3911,15 +3911,15 @@ │ │ │ │ structure("contexts <- rownames(mut_mat)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## See the 'context_potential_damage_analysis()' example for how we obtained the\n", Rd_tag = "RCODE"), │ │ │ │ structure("## context_mismatches:\n", Rd_tag = "RCODE"), │ │ │ │ structure("context_mismatches <- readRDS(system.file(\"states/context_mismatches.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Determine the potential damage per signature\n", Rd_tag = "RCODE"), │ │ │ │ - structure("signature_potential_damage_analysis(signatures, contexts, context_mismatches)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/signature_potential_damage_analysis.Rd", class = "Rd", meta = list( │ │ │ │ + structure("signature_potential_damage_analysis(signatures, contexts, context_mismatches)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/signature_potential_damage_analysis.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ split_muts_region (list) = structure(list(structure(list(structure("Split GRangesList or GRanges based on a list of regions.", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("split_muts_region", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("split_muts_region", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("genomic_regions", Rd_tag = "TEXT")), Rd_tag = "\\concept"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A GRangesList or GRanges object containing variants is split based on a list of regions.\n", Rd_tag = "TEXT"), │ │ │ │ @@ -3970,15 +3970,15 @@ │ │ │ │ structure("## following data:\n", Rd_tag = "RCODE"), │ │ │ │ structure("grl <- readRDS(system.file(\"states/read_vcfs_as_granges_output.rds\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" package = \"MutationalPatterns\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Split muts based on the supplied regions\n", Rd_tag = "RCODE"), │ │ │ │ structure("split_muts_region(grl, regions)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Don't include muts outside of the supplied regions\n", Rd_tag = "RCODE"), │ │ │ │ - structure("split_muts_region(grl, regions, include_other = FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/split_muts_region.Rd", class = "Rd", meta = list( │ │ │ │ + structure("split_muts_region(grl, regions, include_other = FALSE)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/split_muts_region.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ strand_bias_test (list) = structure(list(structure(list(structure("Significance test for strand asymmetry", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("strand_bias_test", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("strand_bias_test", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("This function performs a two sided Poisson test for the ratio between mutations on\n", Rd_tag = "TEXT"), │ │ │ │ structure("each strand. Multiple testing correction is also performed.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -4020,15 +4020,15 @@ │ │ │ │ structure(" p_cutoffs = 0.01, fdr_cutoffs = 0.05\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Use multiple (max 3) significance cutoffs.\n", Rd_tag = "RCODE"), │ │ │ │ structure("## This will vary the number of significance stars.\n", Rd_tag = "RCODE"), │ │ │ │ structure("strand_bias_multistars <- strand_bias_test(strand_counts,\n", Rd_tag = "RCODE"), │ │ │ │ structure(" p_cutoffs = c(0.05, 0.01, 0.005),\n", Rd_tag = "RCODE"), │ │ │ │ structure(" fdr_cutoffs = c(0.1, 0.05, 0.01)\n", Rd_tag = "RCODE"), │ │ │ │ - structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/strand_bias_test.Rd", class = "Rd", meta = list( │ │ │ │ + structure(")\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/strand_bias_test.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ strand_occurrences (list) = structure(list(structure(list(structure("Count occurrences per base substitution type and strand", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("strand_occurrences", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("strand_occurrences", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("For each base substitution type and strand the total number\n", Rd_tag = "TEXT"), │ │ │ │ structure("of mutations and the relative contribution within a group is returned.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -4058,15 +4058,15 @@ │ │ │ │ structure("ref_genome <- \"BSgenome.Hsapiens.UCSC.hg19\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(ref_genome, character.only = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("tissue <- c(\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \"colon\", \"colon\", \"colon\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \"intestine\", \"intestine\", \"intestine\",\n", Rd_tag = "RCODE"), │ │ │ │ structure(" \"liver\", \"liver\", \"liver\"\n", Rd_tag = "RCODE"), │ │ │ │ structure(")\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ - structure("strand_counts <- strand_occurrences(mut_mat_s, by = tissue)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/strand_occurrences.Rd", class = "Rd", meta = list( │ │ │ │ + structure("strand_counts <- strand_occurrences(mut_mat_s, by = tissue)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/strand_occurrences.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ │ │ │ │ │ │ type_context (list) = structure(list(structure(list(structure("Retrieve context of base substitution types", Rd_tag = "TEXT")), Rd_tag = "\\title"), │ │ │ │ structure(list(structure("type_context", Rd_tag = "VERB")), Rd_tag = "\\name"), │ │ │ │ structure(list(structure("type_context", Rd_tag = "VERB")), Rd_tag = "\\alias"), │ │ │ │ structure(list(structure("\n", Rd_tag = "TEXT"), structure("A function to extract the bases 3' upstream and 5' downstream of the base\n", Rd_tag = "TEXT"), │ │ │ │ structure("substitution types.\n", Rd_tag = "TEXT")), Rd_tag = "\\description"), │ │ │ │ @@ -4094,10 +4094,10 @@ │ │ │ │ structure("))\n", Rd_tag = "RCODE"), structure("\n", Rd_tag = "RCODE"), │ │ │ │ structure("## Load the corresponding reference genome.\n", Rd_tag = "RCODE"), │ │ │ │ structure("ref_genome <- \"BSgenome.Hsapiens.UCSC.hg19\"\n", Rd_tag = "RCODE"), │ │ │ │ structure("library(ref_genome, character.only = TRUE)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Get type context\n", Rd_tag = "RCODE"), │ │ │ │ structure("type_context <- type_context(vcfs[[1]], ref_genome)\n", Rd_tag = "RCODE"), │ │ │ │ structure("\n", Rd_tag = "RCODE"), structure("## Get larger type context\n", Rd_tag = "RCODE"), │ │ │ │ - structure("type_context_larger <- type_context(vcfs[[1]], ref_genome, extension = 2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/type_context.Rd", class = "Rd", meta = list( │ │ │ │ + structure("type_context_larger <- type_context(vcfs[[1]], ref_genome, extension = 2)\n", Rd_tag = "RCODE")), Rd_tag = "\\examples")), Rdfile = "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/type_context.Rd", class = "Rd", meta = list( │ │ │ │ docType = character(0), generator = "% Generated by roxygen2: do not edit by hand"), prepared = 3L) │ │ ├── ./usr/lib/R/site-library/MutationalPatterns/help/MutationalPatterns.rdx │ │ │ ├── MutationalPatterns.rdx-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,457 +1,457 @@ │ │ │ │ │ $variables │ │ │ │ │ $variables$`MutationalPatterns-defunct` │ │ │ │ │ -[1] 293 925 │ │ │ │ │ +[1] 309 942 │ │ │ │ │ │ │ │ │ │ $variables$`MutationalPatterns-package` │ │ │ │ │ -[1] 1511 2491 │ │ │ │ │ +[1] 1561 2506 │ │ │ │ │ │ │ │ │ │ $variables$bin_mutation_density │ │ │ │ │ -[1] 4295 2355 │ │ │ │ │ +[1] 4377 2369 │ │ │ │ │ │ │ │ │ │ $variables$binomial_test │ │ │ │ │ -[1] 6940 1178 │ │ │ │ │ +[1] 7053 1192 │ │ │ │ │ │ │ │ │ │ $variables$calculate_lesion_segregation │ │ │ │ │ -[1] 8417 3866 │ │ │ │ │ +[1] 8560 3881 │ │ │ │ │ │ │ │ │ │ $variables$cluster_signatures │ │ │ │ │ -[1] 12577 1545 │ │ │ │ │ +[1] 12751 1561 │ │ │ │ │ │ │ │ │ │ $variables$context_potential_damage_analysis │ │ │ │ │ -[1] 14427 3586 │ │ │ │ │ +[1] 14633 3601 │ │ │ │ │ │ │ │ │ │ $variables$convert_sigs_to_ref │ │ │ │ │ -[1] 18309 1342 │ │ │ │ │ +[1] 18546 1357 │ │ │ │ │ │ │ │ │ │ $variables$cos_sim │ │ │ │ │ -[1] 19938 987 │ │ │ │ │ +[1] 20206 1000 │ │ │ │ │ │ │ │ │ │ $variables$cos_sim_matrix │ │ │ │ │ -[1] 21218 1522 │ │ │ │ │ +[1] 21515 1539 │ │ │ │ │ │ │ │ │ │ $variables$count_dbs_contexts │ │ │ │ │ -[1] 23035 1679 │ │ │ │ │ +[1] 23365 1697 │ │ │ │ │ │ │ │ │ │ $variables$count_indel_contexts │ │ │ │ │ -[1] 25010 1646 │ │ │ │ │ +[1] 25375 1664 │ │ │ │ │ │ │ │ │ │ $variables$count_mbs_contexts │ │ │ │ │ -[1] 26950 1499 │ │ │ │ │ +[1] 27350 1516 │ │ │ │ │ │ │ │ │ │ $variables$determine_regional_similarity │ │ │ │ │ -[1] 28749 4707 │ │ │ │ │ +[1] 29182 4719 │ │ │ │ │ │ │ │ │ │ $variables$enrichment_depletion_test │ │ │ │ │ -[1] 33754 2017 │ │ │ │ │ +[1] 34215 2031 │ │ │ │ │ │ │ │ │ │ $variables$extract_signatures │ │ │ │ │ -[1] 36065 2556 │ │ │ │ │ +[1] 36557 2570 │ │ │ │ │ │ │ │ │ │ $variables$fit_to_signatures │ │ │ │ │ -[1] 38915 1805 │ │ │ │ │ +[1] 39437 1820 │ │ │ │ │ │ │ │ │ │ $variables$fit_to_signatures_bootstrapped │ │ │ │ │ -[1] 41022 3175 │ │ │ │ │ +[1] 41575 3190 │ │ │ │ │ │ │ │ │ │ $variables$fit_to_signatures_strict │ │ │ │ │ -[1] 44496 3417 │ │ │ │ │ +[1] 45080 3430 │ │ │ │ │ │ │ │ │ │ $variables$genomic_distribution │ │ │ │ │ -[1] 48206 3274 │ │ │ │ │ +[1] 48820 3292 │ │ │ │ │ │ │ │ │ │ $variables$get_dbs_context │ │ │ │ │ -[1] 51774 1664 │ │ │ │ │ +[1] 52422 1683 │ │ │ │ │ │ │ │ │ │ $variables$get_indel_context │ │ │ │ │ -[1] 53732 2102 │ │ │ │ │ +[1] 54415 2118 │ │ │ │ │ │ │ │ │ │ $variables$get_known_signatures │ │ │ │ │ -[1] 56131 4062 │ │ │ │ │ +[1] 56847 4076 │ │ │ │ │ │ │ │ │ │ $variables$get_mut_type │ │ │ │ │ -[1] 60485 1876 │ │ │ │ │ +[1] 61231 1891 │ │ │ │ │ │ │ │ │ │ $variables$get_sim_tb │ │ │ │ │ -[1] 62651 1173 │ │ │ │ │ +[1] 63427 1190 │ │ │ │ │ │ │ │ │ │ $variables$lengthen_mut_matrix │ │ │ │ │ -[1] 64121 2113 │ │ │ │ │ +[1] 64930 2127 │ │ │ │ │ │ │ │ │ │ $variables$merge_signatures │ │ │ │ │ -[1] 66527 1663 │ │ │ │ │ +[1] 67366 1679 │ │ │ │ │ │ │ │ │ │ $variables$mut_192_occurrences │ │ │ │ │ -[1] 68488 1239 │ │ │ │ │ +[1] 69358 1253 │ │ │ │ │ │ │ │ │ │ $variables$mut_96_occurrences │ │ │ │ │ -[1] 70023 995 │ │ │ │ │ +[1] 70923 1011 │ │ │ │ │ │ │ │ │ │ $variables$mut_context │ │ │ │ │ -[1] 71308 1621 │ │ │ │ │ +[1] 72240 1635 │ │ │ │ │ │ │ │ │ │ $variables$mut_matrix │ │ │ │ │ -[1] 73219 1654 │ │ │ │ │ +[1] 74180 1669 │ │ │ │ │ │ │ │ │ │ $variables$mut_matrix_stranded │ │ │ │ │ -[1] 75169 2984 │ │ │ │ │ +[1] 76161 2999 │ │ │ │ │ │ │ │ │ │ $variables$mut_strand │ │ │ │ │ -[1] 78443 3051 │ │ │ │ │ +[1] 79465 3066 │ │ │ │ │ │ │ │ │ │ $variables$mut_type │ │ │ │ │ -[1] 81784 1147 │ │ │ │ │ +[1] 82836 1162 │ │ │ │ │ │ │ │ │ │ $variables$mut_type_occurrences │ │ │ │ │ -[1] 83228 1369 │ │ │ │ │ +[1] 84312 1384 │ │ │ │ │ │ │ │ │ │ $variables$mutations_from_vcf │ │ │ │ │ -[1] 84889 1113 │ │ │ │ │ +[1] 86004 1128 │ │ │ │ │ │ │ │ │ │ $variables$plot_192_profile │ │ │ │ │ -[1] 86297 1886 │ │ │ │ │ +[1] 87442 1901 │ │ │ │ │ │ │ │ │ │ $variables$plot_96_profile │ │ │ │ │ -[1] 88478 1850 │ │ │ │ │ +[1] 89653 1865 │ │ │ │ │ │ │ │ │ │ $variables$plot_bootstrapped_contribution │ │ │ │ │ -[1] 90628 1619 │ │ │ │ │ +[1] 91833 1634 │ │ │ │ │ │ │ │ │ │ $variables$plot_compare_dbs │ │ │ │ │ -[1] 92541 2795 │ │ │ │ │ +[1] 93777 2811 │ │ │ │ │ │ │ │ │ │ $variables$plot_compare_indels │ │ │ │ │ -[1] 95631 2778 │ │ │ │ │ +[1] 96900 2794 │ │ │ │ │ │ │ │ │ │ $variables$plot_compare_mbs │ │ │ │ │ -[1] 98702 2603 │ │ │ │ │ +[1] 100004 2619 │ │ │ │ │ │ │ │ │ │ $variables$plot_compare_profiles │ │ │ │ │ -[1] 101601 2802 │ │ │ │ │ +[1] 102936 2818 │ │ │ │ │ │ │ │ │ │ $variables$plot_contribution │ │ │ │ │ -[1] 104694 2661 │ │ │ │ │ +[1] 106062 2677 │ │ │ │ │ │ │ │ │ │ $variables$plot_contribution_heatmap │ │ │ │ │ -[1] 107653 2792 │ │ │ │ │ +[1] 109053 2807 │ │ │ │ │ │ │ │ │ │ $variables$plot_correlation_bootstrap │ │ │ │ │ -[1] 110743 1435 │ │ │ │ │ +[1] 112174 1451 │ │ │ │ │ │ │ │ │ │ $variables$plot_cosine_heatmap │ │ │ │ │ -[1] 112474 2801 │ │ │ │ │ +[1] 113937 2815 │ │ │ │ │ │ │ │ │ │ $variables$plot_dbs_contexts │ │ │ │ │ -[1] 115570 2014 │ │ │ │ │ +[1] 117063 2027 │ │ │ │ │ │ │ │ │ │ $variables$plot_enrichment_depletion │ │ │ │ │ -[1] 117883 2023 │ │ │ │ │ +[1] 119404 2037 │ │ │ │ │ │ │ │ │ │ $variables$plot_indel_contexts │ │ │ │ │ -[1] 120202 2575 │ │ │ │ │ +[1] 121753 2591 │ │ │ │ │ │ │ │ │ │ $variables$plot_lesion_segregation │ │ │ │ │ -[1] 123075 2794 │ │ │ │ │ +[1] 124657 2808 │ │ │ │ │ │ │ │ │ │ $variables$plot_main_dbs_contexts │ │ │ │ │ -[1] 126168 1911 │ │ │ │ │ +[1] 127780 1927 │ │ │ │ │ │ │ │ │ │ $variables$plot_main_indel_contexts │ │ │ │ │ -[1] 128379 1916 │ │ │ │ │ +[1] 130023 1930 │ │ │ │ │ │ │ │ │ │ $variables$plot_mbs_contexts │ │ │ │ │ -[1] 130590 1674 │ │ │ │ │ +[1] 132264 1691 │ │ │ │ │ │ │ │ │ │ $variables$plot_original_vs_reconstructed │ │ │ │ │ -[1] 132567 1949 │ │ │ │ │ +[1] 134273 1964 │ │ │ │ │ │ │ │ │ │ $variables$plot_profile_heatmap │ │ │ │ │ -[1] 134812 2087 │ │ │ │ │ +[1] 136549 2100 │ │ │ │ │ │ │ │ │ │ $variables$plot_profile_region │ │ │ │ │ -[1] 137195 2216 │ │ │ │ │ +[1] 138960 2229 │ │ │ │ │ │ │ │ │ │ $variables$plot_rainfall │ │ │ │ │ -[1] 139703 2799 │ │ │ │ │ +[1] 141496 2814 │ │ │ │ │ │ │ │ │ │ $variables$plot_regional_similarity │ │ │ │ │ -[1] 142801 2980 │ │ │ │ │ +[1] 144625 2997 │ │ │ │ │ │ │ │ │ │ $variables$plot_river │ │ │ │ │ -[1] 146071 1621 │ │ │ │ │ +[1] 147927 1636 │ │ │ │ │ │ │ │ │ │ $variables$plot_signature_strand_bias │ │ │ │ │ -[1] 147993 1497 │ │ │ │ │ +[1] 149879 1514 │ │ │ │ │ │ │ │ │ │ $variables$plot_spectrum │ │ │ │ │ -[1] 149782 3134 │ │ │ │ │ +[1] 151700 3149 │ │ │ │ │ │ │ │ │ │ $variables$plot_spectrum_region │ │ │ │ │ -[1] 153213 4322 │ │ │ │ │ +[1] 155162 4347 │ │ │ │ │ │ │ │ │ │ $variables$plot_strand │ │ │ │ │ -[1] 157825 1896 │ │ │ │ │ +[1] 159815 1911 │ │ │ │ │ │ │ │ │ │ $variables$plot_strand_bias │ │ │ │ │ -[1] 160014 2009 │ │ │ │ │ +[1] 162035 2025 │ │ │ │ │ │ │ │ │ │ $variables$pool_mut_mat │ │ │ │ │ -[1] 162314 1153 │ │ │ │ │ +[1] 164367 1168 │ │ │ │ │ │ │ │ │ │ $variables$read_vcfs_as_granges │ │ │ │ │ -[1] 163765 3697 │ │ │ │ │ +[1] 165849 3711 │ │ │ │ │ │ │ │ │ │ $variables$`region_cossim-class` │ │ │ │ │ -[1] 167756 1956 │ │ │ │ │ +[1] 169871 1975 │ │ │ │ │ │ │ │ │ │ $variables$rename_nmf_signatures │ │ │ │ │ -[1] 170008 2330 │ │ │ │ │ +[1] 172159 2346 │ │ │ │ │ │ │ │ │ │ $variables$`show-region_cossim-method` │ │ │ │ │ -[1] 172638 746 │ │ │ │ │ +[1] 174821 762 │ │ │ │ │ │ │ │ │ │ $variables$signature_potential_damage_analysis │ │ │ │ │ -[1] 173691 2500 │ │ │ │ │ +[1] 175905 2516 │ │ │ │ │ │ │ │ │ │ $variables$split_muts_region │ │ │ │ │ -[1] 176486 2219 │ │ │ │ │ +[1] 178731 2235 │ │ │ │ │ │ │ │ │ │ $variables$strand_bias_test │ │ │ │ │ -[1] 178998 2002 │ │ │ │ │ +[1] 181275 2017 │ │ │ │ │ │ │ │ │ │ $variables$strand_occurrences │ │ │ │ │ -[1] 181294 1685 │ │ │ │ │ +[1] 183602 1700 │ │ │ │ │ │ │ │ │ │ $variables$type_context │ │ │ │ │ -[1] 183271 1631 │ │ │ │ │ +[1] 185610 1645 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $references │ │ │ │ │ $references$`env::1` │ │ │ │ │ -[1] 0 293 │ │ │ │ │ +[1] 0 309 │ │ │ │ │ │ │ │ │ │ $references$`env::10` │ │ │ │ │ -[1] 20925 293 │ │ │ │ │ +[1] 21206 309 │ │ │ │ │ │ │ │ │ │ $references$`env::11` │ │ │ │ │ -[1] 22740 295 │ │ │ │ │ +[1] 23054 311 │ │ │ │ │ │ │ │ │ │ $references$`env::12` │ │ │ │ │ -[1] 24714 296 │ │ │ │ │ +[1] 25062 313 │ │ │ │ │ │ │ │ │ │ $references$`env::13` │ │ │ │ │ -[1] 26656 294 │ │ │ │ │ +[1] 27039 311 │ │ │ │ │ │ │ │ │ │ $references$`env::14` │ │ │ │ │ -[1] 28449 300 │ │ │ │ │ +[1] 28866 316 │ │ │ │ │ │ │ │ │ │ $references$`env::15` │ │ │ │ │ -[1] 33456 298 │ │ │ │ │ +[1] 33901 314 │ │ │ │ │ │ │ │ │ │ $references$`env::16` │ │ │ │ │ -[1] 35771 294 │ │ │ │ │ +[1] 36246 311 │ │ │ │ │ │ │ │ │ │ $references$`env::17` │ │ │ │ │ -[1] 38621 294 │ │ │ │ │ +[1] 39127 310 │ │ │ │ │ │ │ │ │ │ $references$`env::18` │ │ │ │ │ -[1] 40720 302 │ │ 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$references$`env::9` │ │ │ │ │ -[1] 19651 287 │ │ │ │ │ +[1] 19903 303 │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ $compressed │ │ │ │ │ [1] TRUE │ │ ├── ./usr/lib/R/site-library/MutationalPatterns/help/paths.rds │ │ │ ├── paths.rds-content │ │ │ │ ├── Rscript --vanilla -e 'args <- commandArgs(TRUE); readRDS(args[1])' {} │ │ │ │ │ @@ -1,77 +1,77 @@ │ │ │ │ │ - [1] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/MutationalPatterns-defunct.Rd" │ │ │ │ │ - [2] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/MutationalPatterns-package.Rd" │ │ │ │ │ - [3] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/bin_mutation_density.Rd" │ │ │ │ │ - [4] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/binomial_test.Rd" │ │ │ │ │ - [5] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/calculate_lesion_segregation.Rd" │ │ │ │ │ - [6] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/cluster_signatures.Rd" │ │ │ │ │ - [7] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/context_potential_damage_analysis.Rd" │ │ │ │ │ - [8] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/convert_sigs_to_ref.Rd" │ │ │ │ │ - [9] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/cos_sim.Rd" │ │ │ │ │ -[10] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/cos_sim_matrix.Rd" │ │ │ │ │ -[11] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/count_dbs_contexts.Rd" │ │ │ │ │ -[12] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/count_indel_contexts.Rd" │ │ │ │ │ -[13] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/count_mbs_contexts.Rd" │ │ │ │ │ -[14] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/determine_regional_similarity.Rd" │ │ │ │ │ -[15] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/enrichment_depletion_test.Rd" │ │ │ │ │ -[16] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/extract_signatures.Rd" │ │ │ │ │ -[17] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/fit_to_signatures.Rd" │ │ │ │ │ -[18] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/fit_to_signatures_bootstrapped.Rd" │ │ │ │ │ -[19] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/fit_to_signatures_strict.Rd" │ │ │ │ │ -[20] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/genomic_distribution.Rd" │ │ │ │ │ -[21] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/get_dbs_context.Rd" │ │ │ │ │ -[22] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/get_indel_context.Rd" │ │ │ │ │ -[23] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/get_known_signatures.Rd" │ │ │ │ │ -[24] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/get_mut_type.Rd" │ │ │ │ │ -[25] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/get_sim_tb.Rd" │ │ │ │ │ -[26] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/lengthen_mut_matrix.Rd" │ │ │ │ │ -[27] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/merge_signatures.Rd" │ │ │ │ │ -[28] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_192_occurrences.Rd" │ │ │ │ │ -[29] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_96_occurrences.Rd" │ │ │ │ │ -[30] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_context.Rd" │ │ │ │ │ -[31] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_matrix.Rd" │ │ │ │ │ -[32] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_matrix_stranded.Rd" │ │ │ │ │ -[33] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_strand.Rd" │ │ │ │ │ -[34] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_type.Rd" │ │ │ │ │ -[35] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mut_type_occurrences.Rd" │ │ │ │ │ -[36] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/mutations_from_vcf.Rd" │ │ │ │ │ -[37] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_192_profile.Rd" │ │ │ │ │ -[38] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_96_profile.Rd" │ │ │ │ │ -[39] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_bootstrapped_contribution.Rd" │ │ │ │ │ -[40] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_compare_dbs.Rd" │ │ │ │ │ -[41] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_compare_indels.Rd" │ │ │ │ │ -[42] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_compare_mbs.Rd" │ │ │ │ │ -[43] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_compare_profiles.Rd" │ │ │ │ │ -[44] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_contribution.Rd" │ │ │ │ │ -[45] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_contribution_heatmap.Rd" │ │ │ │ │ -[46] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_correlation_bootstrap.Rd" │ │ │ │ │ -[47] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_cosine_heatmap.Rd" │ │ │ │ │ -[48] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_dbs_contexts.Rd" │ │ │ │ │ -[49] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_enrichment_depletion.Rd" │ │ │ │ │ -[50] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_indel_contexts.Rd" │ │ │ │ │ -[51] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_lesion_segregation.Rd" │ │ │ │ │ -[52] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_main_dbs_contexts.Rd" │ │ │ │ │ -[53] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_main_indel_contexts.Rd" │ │ │ │ │ -[54] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_mbs_contexts.Rd" │ │ │ │ │ -[55] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_original_vs_reconstructed.Rd" │ │ │ │ │ -[56] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_profile_heatmap.Rd" │ │ │ │ │ -[57] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_profile_region.Rd" │ │ │ │ │ -[58] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_rainfall.Rd" │ │ │ │ │ -[59] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_regional_similarity.Rd" │ │ │ │ │ -[60] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_river.Rd" │ │ │ │ │ -[61] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_signature_strand_bias.Rd" │ │ │ │ │ -[62] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_spectrum.Rd" │ │ │ │ │ -[63] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_spectrum_region.Rd" │ │ │ │ │ -[64] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_strand.Rd" │ │ │ │ │ -[65] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/plot_strand_bias.Rd" │ │ │ │ │ -[66] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/pool_mut_mat.Rd" │ │ │ │ │ -[67] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/read_vcfs_as_granges.Rd" │ │ │ │ │ -[68] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/region_cossim-class.Rd" │ │ │ │ │ -[69] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/rename_nmf_signatures.Rd" │ │ │ │ │ -[70] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/show-region_cossim-method.Rd" │ │ │ │ │ -[71] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/signature_potential_damage_analysis.Rd" │ │ │ │ │ -[72] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/split_muts_region.Rd" │ │ │ │ │ -[73] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/strand_bias_test.Rd" │ │ │ │ │ -[74] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/strand_occurrences.Rd" │ │ │ │ │ -[75] "/home/moeller/Salsa/r-bioc-mutationalpatterns/man/type_context.Rd" │ │ │ │ │ + [1] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/MutationalPatterns-defunct.Rd" │ │ │ │ │ + [2] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/MutationalPatterns-package.Rd" │ │ │ │ │ + [3] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/bin_mutation_density.Rd" │ │ │ │ │ + [4] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/binomial_test.Rd" │ │ │ │ │ + [5] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/calculate_lesion_segregation.Rd" │ │ │ │ │ + [6] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/cluster_signatures.Rd" │ │ │ │ │ + [7] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/context_potential_damage_analysis.Rd" │ │ │ │ │ + [8] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/convert_sigs_to_ref.Rd" │ │ │ │ │ + [9] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/cos_sim.Rd" │ │ │ │ │ +[10] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/cos_sim_matrix.Rd" │ │ │ │ │ +[11] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/count_dbs_contexts.Rd" │ │ │ │ │ +[12] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/count_indel_contexts.Rd" │ │ │ │ │ +[13] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/count_mbs_contexts.Rd" │ │ │ │ │ +[14] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/determine_regional_similarity.Rd" │ │ │ │ │ +[15] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/enrichment_depletion_test.Rd" │ │ │ │ │ +[16] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/extract_signatures.Rd" │ │ │ │ │ +[17] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/fit_to_signatures.Rd" │ │ │ │ │ +[18] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/fit_to_signatures_bootstrapped.Rd" │ │ │ │ │ +[19] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/fit_to_signatures_strict.Rd" │ │ │ │ │ +[20] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/genomic_distribution.Rd" │ │ │ │ │ +[21] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/get_dbs_context.Rd" │ │ │ │ │ +[22] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/get_indel_context.Rd" │ │ │ │ │ +[23] "/build/reproducible-path/r-bioc-mutationalpatterns-3.22.0+dfsg/man/get_known_signatures.Rd" │ │ │ │ │ +[24] 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