plotObsExpWSAFPlotly {DEploid} | R Documentation |
Plot observed alternative allele frequency within sample against expected WSAF.
plotObsExpWSAFPlotly(obsWSAF, expWSAF, title = "WSAF(observed vs expected)")
obsWSAF |
Numeric array of observed WSAF. |
expWSAF |
Numeric array of expected WSAF. |
title |
Figure title, "WSAF(observed vs expected)" by default |
## 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")
PG0390CoverageV.deconv = dEploid(paste("-vcf", vcfFile,
"-plaf", plafFile, "-noPanel"))
prop = PG0390CoverageV.deconv$Proportions[dim(PG0390CoverageV.deconv
$Proportions)[1],]
expWSAF = t(PG0390CoverageV.deconv$Haps) %*% prop
plotObsExpWSAFPlotly(obsWSAF, expWSAF)
## End(Not run)