diff --git a/DESCRIPTION b/DESCRIPTION index 3cb5f21..8d6df0a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,8 +2,8 @@ Package: PureCN Type: Package Title: Copy number calling and SNV classification using targeted short read sequencing -Version: 2.11.0 -Date: 2024-04-24 +Version: 2.11.1 +Date: 2024-05-10 Authors@R: c(person("Markus", "Riester", role = c("aut", "cre"), email = "markus.riester@novartis.com", diff --git a/NEWS b/NEWS index 7cc1eff..db30669 100755 --- a/NEWS +++ b/NEWS @@ -1,3 +1,14 @@ +Changes in version 2.12.0 +------------------------- + +NEW FEATURES + + o Added --num-eigen-vectors to PureCN.R to set the number of eigen vectors. + Tuning parameter for coverage normalization. Default should in most cases + be a good compromise between removing most normal noise and not + overfitting to pool of normal samples. + + Changes in version 2.10.0 ------------------------- diff --git a/inst/extdata/PureCN.R b/inst/extdata/PureCN.R index 0ce5c3d..14a7765 100644 --- a/inst/extdata/PureCN.R +++ b/inst/extdata/PureCN.R @@ -71,6 +71,9 @@ option_list <- list( make_option(c("--min-fraction-offtarget"), action = "store", type = "double", default = formals(PureCN::filterIntervals)$min.fraction.offtarget, help = "Interval Filter: Ignore off-target internals when only the specified fraction of all intervals are off-target intervals [default %default]"), + make_option(c("--num-eigen-vectors"), action = "store", type = "integer", + default = formals(PureCN::calculateTangentNormal)$num.eigen, + help = "Coverage Normalization: Number of eigen vectors when --normaldb is provided [default %default]"), make_option(c("--fun-segmentation"), action = "store", type = "character", default = "CBS", help = "Segmentation: Algorithm. CBS, PSCBS, GATK4, Hclust, or none [default %default]"), make_option(c("--alpha"), action = "store", type = "double", @@ -283,7 +286,7 @@ if (file.exists(file.rds) && !opt$force) { if (!is.null(normalDB)) { if (is.null(normal.coverage.file)) { normal.coverage.file <- calculateTangentNormal(tumor.coverage.file, - normalDB) + normalDB, num.eigen = opt[["num_eigen_vectors"]]) } } else if (is.null(normal.coverage.file) && is.null(seg.file) && is.null(log.ratio)) {