DEploid (version 0.5.7)

plotWSAFVsPLAFPlotly: Plot WSAF vs PLAF

Description

Plot allele frequencies within sample against population level.

Usage

plotWSAFVsPLAFPlotly(
  plaf,
  obsWSAF,
  ref,
  alt,
  title = "WSAF vs PLAF",
  potentialOutliers = c()
)

Arguments

plaf

Numeric array of population level allele frequency.

obsWSAF

Numeric array of observed altenative allele frequencies within sample.

ref

Numeric array of reference allele count.

alt

Numeric array of alternative allele count.

title

Figure title, "WSAF vs PLAF" by default

potentialOutliers

Index of potential outliers.

Examples

# Example 1
refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
PG0390CoverageT <- extractCoverageFromTxt(refFile, altFile)
obsWSAF <- computeObsWSAF(PG0390CoverageT$altCount, PG0390CoverageT$refCount)
plafFile <- system.file("extdata", "labStrains.test.PLAF.txt",
  package = "DEploid"
)
plaf <- extractPLAF(plafFile)
plotWSAFVsPLAFPlotly(
  plaf, obsWSAF, PG0390CoverageT$refCount,
  PG0390CoverageT$altCount
)

# Example 2
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"
)
plaf <- extractPLAF(plafFile)
plotWSAFVsPLAFPlotly(
  plaf, obsWSAF, PG0390CoverageV$refCount,
  PG0390CoverageV$altCount
)