plotObsExpWSAF: Plot WSAF

In DEploid: Deconvolute Mixed Genomes with Unknown Proportions

Description

Plot observed alternative allele frequency within sample against expected WSAF.

Usage

plotObsExpWSAF(
  obsWSAF,
  expWSAF,
  title = "WSAF(observed vs expected)",
  cex.lab = 1,
  cex.main = 1,
  cex.axis = 1
)

Arguments

obsWSAF	Numeric array of observed WSAF.
expWSAF	Numeric array of expected WSAF.
title	Figure title.
cex.lab	Label size.
cex.main	Title size.
cex.axis	Axis text size.

Examples

## Not run: 
vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
PG0390CoverageV = extractCoverageFromVcf(vcfFile)
obsWSAF = computeObsWSAF(PG0390CoverageV$altCount, PG0390CoverageV$refCount)
plafFile = system.file("extdata", "labStrains.test.PLAF.txt",
 package = "DEploid")
PG0390.deconv = dEploid(paste("-vcf", vcfFile,
                                       "-plaf", plafFile, "-noPanel"))
prop = PG0390.deconv$Proportions[dim(PG0390.deconv$Proportions)[1],]
expWSAF = t(PG0390.deconv$Haps) %*% prop
plotObsExpWSAF(obsWSAF, expWSAF)

## End(Not run)

DEploid documentation built on April 22, 2020, 1:04 a.m.