plotWSAFvsPLAF {DEploid.utils} | R Documentation |
Plot WSAF vs PLAF
Description
Plot allele frequencies within sample against population level.
Usage
plotWSAFvsPLAF(
plaf,
obsWSAF,
expWSAF = c(),
potentialOutliers = c(),
title = "WSAF vs PLAF",
cex.lab = 1,
cex.main = 1,
cex.axis = 1
)
Arguments
plaf |
Numeric array of population level allele frequency. |
obsWSAF |
Numeric array of observed altenative allele frequencies within sample. |
expWSAF |
Numeric array of expected WSAF from model. |
potentialOutliers |
Potential outliers |
title |
Figure title, "WSAF vs PLAF" by default |
cex.lab |
Label size. |
cex.main |
Title size. |
cex.axis |
Axis text size. |
Value
No return value called for side effects
Examples
# Example 1
refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid.utils")
altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid.utils")
PG0390CoverageTxt <- extractCoverageFromTxt(refFile, altFile)
obsWSAF <- computeObsWSAF(PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount)
plafFile <- system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid.utils")
plaf <- extractPLAF(plafFile)
plotWSAFvsPLAF(plaf, obsWSAF)
# Example 2
vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFile, "PG0390-C")
obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount, PG0390CoverageVcf$refCount)
plafFile <- system.file("extdata", "labStrains.test.PLAF.txt", package = "DEploid.utils")
plaf <- extractPLAF(plafFile)
plotWSAFvsPLAF(plaf, obsWSAF)
[Package DEploid.utils version 0.0.1 Index]