@@ -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 = "[email protected]",

@@ -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

 -------------------------

@@ -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)) {