DEploid (version 0.5.4)

plotObsExpWSAF: Plot WSAF

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

if (FALSE) {
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)
}