plotObsExpWSAFPlotly: Plot WSAF

In DEploid: Deconvolute Mixed Genomes with Unknown Proportions

Plot WSAF

Description

Plot observed alternative allele frequency within sample against expected WSAF.

Usage

plotObsExpWSAFPlotly(obsWSAF, expWSAF, title = "WSAF(observed vs expected)")

Arguments

obsWSAF	Numeric array of observed WSAF.
expWSAF	Numeric array of expected WSAF.
title	Figure title, "WSAF(observed vs expected)" by default

Examples

## Not run: 
vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
PG0390CoverageV <- extractCoverageFromVcf(vcfFile, "PG0390-C")
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)

DEploid documentation built on April 4, 2025, 2:16 a.m.