histWSAF {DEploid.utils} | R Documentation |
WSAF histogram
Description
Produce histogram of the allele frequency within sample.
Usage
histWSAF(
obsWSAF,
exclusive = TRUE,
title = "Histogram 0<WSAF<1",
cex.lab = 1,
cex.main = 1,
cex.axis = 1
)
Arguments
obsWSAF |
Observed allele frequency within sample |
exclusive |
When TRUE 0 < WSAF < 1; otherwise 0 <= WSAF <= 1. |
title |
Histogram title |
cex.lab |
Label size. |
cex.main |
Title size. |
cex.axis |
Axis text size. |
Value
histogram
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)
histWSAF(obsWSAF)
myhist <- histWSAF(obsWSAF, FALSE)
# 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)
histWSAF(obsWSAF)
myhist <- histWSAF(obsWSAF, FALSE)
[Package DEploid.utils version 0.0.1 Index]