Adding new doc

R/util.R

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+#' Concatenate split files
+#' 
+#' Convenience function to concatenate a series of files specified in a file of file names.
+#' This function assumes all files have the same layout.
+#' @param fofn A file of file names to be concatenated
+#' @param inputdir Full path to where the input files are stored
+#' @param outfile Full path to where the output should be written
+#' @param haveHeader Boolean that specifies whether the input files have a header
+#' @author sd11
+#' @export
+concat_files = function(fofn, inputdir, outfile, haveHeader) {
+
+  inputdir = paste(inputdir,"/", sep="")
+  list_of_files = read.table(fofn, stringsAsFactors=F, header=F)[,1]
+
+  output = data.frame()
+  for (infile in list_of_files) {
+    infile = paste(inputdir, infile, sep="")
+    # Check if file is there and it contains data
+    if (file.exists(infile) & file.info(infile)$size != 0) {
+      dat = read.delim(infile, header=haveHeader, quote=NULL, stringsAsFactors=F)
+      output = rbind(output, dat)
+    }
+  }
+
+  write.table(output, file=outfile, col.names=haveHeader, row.names=F, sep="\t", quote=F)
+}
+
+#' Split a file per chromosome
+#'
+#' Convenience function to split an input file per chromosome. All it requires is that
+#' the infile has as first column chromosome specification. The output files will be named
+#' outdir/prefixCHROMNUMBERpostfix
+#' @param infile The file to be split
+#' @param prefix Prefix of the output file
+#' @param postfix Postfix of the output file
+#' @param outdir Directory where the output files are to be written
+#' @param chrom_file A simple list of chromosomes to be considered
+#' @author sd11
+#' @export
+split_by_chrom = function(infile, prefix, postfix, outdir, chrom_file) {
+  outdir = paste(outdir, "/", sep="")
+
+  # Check if there are lines in the file, otherwise it will crash this script
+  if (file.info(infile)$size == 0) {
+    print("No lines in loci file")
+    q(save="no")
+  }
+
+  loci = read.delim(infile, stringsAsFactors=F, header=F)
+
+  chroms = read.delim(chrom_file, stringsAsFactors=F, header=F)
+
+  for (i in 1:nrow(chroms)) {
+    selection = loci[loci[,1]==chroms[i,1],]
+    chrom_id = chroms[i,2]
+    write.table(selection, file=paste(outdir, prefix, chrom_id, postfix, sep=""), quote=F, row.names=F, col.names=F, sep="\t")
+  }
+}
+
+#' Calculate power to call subclones. 
+#' 
+#' This function calculates the 
+#' average number of reads per clonal chromosome copy.
+#' @param purity The sample purity
+#' @param ploidy The tumour ploidy
+#' @param coverage The tumour sample coverage
+#' @return The average reads per chromosome copy, a.k.a. power
+#' @author sd11
+calc_power = function(purity, ploidy, coverage) {
+  return(round((purity) / (purity*ploidy + (1-purity)*2) * coverage, 3))
+}

man/calc_power.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/util.R
+\name{calc_power}
+\alias{calc_power}
+\title{Calculate power to call subclones.}
+\usage{
+calc_power(purity, ploidy, coverage)
+}
+\arguments{
+\item{purity}{The sample purity}
+
+\item{ploidy}{The tumour ploidy}
+
+\item{coverage}{The tumour sample coverage}
+}
+\value{
+The average reads per chromosome copy, a.k.a. power
+}
+\description{
+This function calculates the
+average number of reads per clonal chromosome copy.
+}
+\author{
+sd11
+}
+

man/createPng.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/qualitycontrol.R
+\name{createPng}
+\alias{createPng}
+\title{Create a PNG file}
+\usage{
+createPng(p, filename, width, height)
+}
+\arguments{
+\item{p}{The figure}
+
+\item{filename}{Where to save the image}
+
+\item{width}{Width}
+
+\item{height}{Height}
+}
+\description{
+Create a PNG file
+}
+

man/plot_ccf_hist.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/qualitycontrol.R
+\name{plot_ccf_hist}
+\alias{plot_ccf_hist}
+\title{Plot cancer cell fraction histogram}
+\usage{
+plot_ccf_hist(data, samplename, outdir)
+}
+\arguments{
+\item{data}{A DPClust input table}
+
+\item{samplename}{Name of the sample}
+
+\item{outdir}{Directory where the figure is to be stored}
+}
+\description{
+Plot cancer cell fraction histogram
+}
+\author{
+sd11
+}
+

man/plot_mcn_hist.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/qualitycontrol.R
+\name{plot_mcn_hist}
+\alias{plot_mcn_hist}
+\title{Plot mutation copy number histogram}
+\usage{
+plot_mcn_hist(data, samplename, outdir)
+}
+\arguments{
+\item{data}{A DPClust input table}
+
+\item{samplename}{Name of the sample}
+
+\item{outdir}{Directory where the figure is to be stored}
+}
+\description{
+Plot mutation copy number histogram
+}
+\author{
+sd11
+}
+

man/plot_vaf_hist.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/qualitycontrol.R
+\name{plot_vaf_hist}
+\alias{plot_vaf_hist}
+\title{Plot allele frequency histogram}
+\usage{
+plot_vaf_hist(data, samplename, outdir)
+}
+\arguments{
+\item{data}{A DPClust input table}
+
+\item{samplename}{Name of the sample}
+
+\item{outdir}{Directory where the figure is to be stored}
+}
+\description{
+Plot allele frequency histogram
+}
+\author{
+sd11
+}
+