@@ -69,4 +69,4 @@ biocViews: CopyNumberVariation, Software, Sequencing,

     VariantAnnotation, VariantDetection, Coverage, ImmunoOncology

 NeedsCompilation: no

 ByteCompile: yes

-RoxygenNote: 7.2.3.9000

+RoxygenNote: 7.3.1

@@ -1,5 +1,6 @@

 # Generated by roxygen2: do not edit by hand

+export(adjustLogRatio)

 export(annotateTargets)

 export(bootstrapResults)

 export(calculateBamCoverageByInterval)

@@ -1,6 +1,12 @@

 Changes in version 2.10.0

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

+NEW FEATURES

+    o adjustLogRatio function for adjusting a tumor vs normal coverage

+      ratio for purity and ploidy. Useful for downstream tools that

+      expect ratios instead of absolute copy numbers such as GISTIC.

+      Thanks @tedtoal (#40).

+

 SIGNIFICANT USER-VISIBLE CHANGES

     o Provide interval-level likelihood scores in runAbsoluteCN return

new file mode 100644

@@ -0,0 +1,40 @@

+#' Adjust tumor vs. normal coverage log ratio for tumor purity and ploidy

+#' 

+#' This function can be used to adjust the log ratio for tumor purity and

+#' ploidy for downstream tools that expect a log2 ratio (for example GISTIC).

+#' 

+#' 

+#' @param ratio Vector of log2 tumor vs normal coverage ratios. 

+#' @param purity Purity of sample.

+#' @param ploidy Ploidy of sample.

+#' @param is.log2 \code{log.ratio} is \code{log2} transformed. 

+#' @param min.ratio Minimum (non-log2-transformed) ratio. Set to approx -8

+#' \code{log2} adjusted.

+#' @return \code{numeric(length(log.ratio))}, \code{log.ratio} adjusted 

+#' for \code{purity} and \code{ploidy} 

+#' @author Markus Riester

+#' @references

+#   * Zack et al. (2012), Pan-cancer patterns of somatic copy number alteration 

+#'    Nature Biotechnology.

+#'  * Toal (2018), https://github.com/lima1/PureCN/issues/40

+#' 

+#' @examples

+#' 

+#' normal.coverage.file <- system.file("extdata", "example_normal.txt.gz", 

+#'     package = "PureCN")

+#' tumor.coverage.file <- system.file("extdata", "example_tumor.txt.gz", 

+#'     package = "PureCN")

+#' normal <- readCoverageFile(normal.coverage.file)

+#' tumor <- readCoverageFile(tumor.coverage.file)

+#' log.ratio <- calculateLogRatio(normal, tumor)

+#' log.ratio.adjusted <- adjustLogRatio(log.ratio, 0.65, 1.73)

+#' 

+#' @export adjustLogRatio

+adjustLogRatio <- function(ratio, purity, ploidy, is.log2 = TRUE, min.ratio = 2^-8) {

+    if (is.log2) ratio <- 2^ratio

+    adjusted <- (purity * ploidy * ratio + 2 * (1 - purity) * ratio - 2 * (1 - purity)) / (purity * ploidy)

+    adjusted <- pmax(min.ratio, adjusted)

+    if (is.log2) adjusted <- log2(adjusted)

+    return(adjusted)

+}

+

new file mode 100644

@@ -0,0 +1,47 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/adjustLogRatio.R

+\name{adjustLogRatio}

+\alias{adjustLogRatio}

+\title{Adjust tumor vs. normal coverage log ratio for tumor purity and ploidy}

+\usage{

+adjustLogRatio(ratio, purity, ploidy, is.log2 = TRUE, min.ratio = 2^-8)

+}

+\arguments{

+\item{ratio}{Vector of log2 tumor vs normal coverage ratios.}

+

+\item{purity}{Purity of sample.}

+

+\item{ploidy}{Ploidy of sample.}

+

+\item{is.log2}{\code{log.ratio} is \code{log2} transformed.}

+

+\item{min.ratio}{Minimum (non-log2-transformed) ratio. Set to approx -8

+\code{log2} adjusted.}

+}

+\value{

+\code{numeric(length(log.ratio))}, \code{log.ratio} adjusted 

+for \code{purity} and \code{ploidy}

+}

+\description{

+This function can be used to adjust the log ratio for tumor purity and

+ploidy for downstream tools that expect a log2 ratio (for example GISTIC).

+}

+\examples{

+

+normal.coverage.file <- system.file("extdata", "example_normal.txt.gz", 

+    package = "PureCN")

+tumor.coverage.file <- system.file("extdata", "example_tumor.txt.gz", 

+    package = "PureCN")

+normal <- readCoverageFile(normal.coverage.file)

+tumor <- readCoverageFile(tumor.coverage.file)

+log.ratio <- calculateLogRatio(normal, tumor)

+log.ratio.adjusted <- adjustLogRatio(log.ratio, 0.65, 1.73)

+

+}

+\references{

+Nature Biotechnology.

+ * Toal (2018), https://github.com/lima1/PureCN/issues/40

+}

+\author{

+Markus Riester

+}

@@ -7,9 +7,9 @@

 filterVcfMuTect2(

   vcf,

   tumor.id.in.vcf = NULL,

-  ignore = c("clustered_events", "t_lod", "str_contraction", "read_position",

-    "position", "fragment_length", "multiallelic", "clipping", "strand_artifact",

-    "strand_bias", "slippage", "weak_evidence", "orientation", "haplotype"),

+  ignore = c("clustered_events", "t_lod", "str_contraction", "read_position", "position",

+    "fragment_length", "multiallelic", "clipping", "strand_artifact", "strand_bias",

+    "slippage", "weak_evidence", "orientation", "haplotype"),

   ...

 )

 }

new file mode 100644

@@ -0,0 +1,16 @@

+context("adjustLogRatio")

+

+test_that("Function returns expected values for example coverage", {

+     data(purecn.example.output)

+     log.ratio <- purecn.example.output$results[[1]]$seg$seg.mean   

+     purity <- purecn.example.output$results[[1]]$purity

+     ploidy <- purecn.example.output$results[[1]]$ploidy

+     log.ratio.adjusted <- adjustLogRatio(log.ratio, purity, ploidy)

+     total.ploidy <- 1.73

+     p <- 1

+     log.ratio.offset <- 0

+     opt.C <- (2^(log.ratio.adjusted + log.ratio.offset) *  total.ploidy)/p - ((2 * (1 - p))/p)

+     expect_lt(abs(min(log.ratio.adjusted, na.rm=TRUE) + 8), 0.001)

+     expect_lt(median(abs(opt.C - purecn.example.output$results[[1]]$seg$C)), 0.1)  

+})

+