DEploid.utils (version 0.0.1)

histWSAF: WSAF histogram

Description

Produce histogram of the allele frequency within sample.

Usage

histWSAF(
  obsWSAF,
  exclusive = TRUE,
  title = "Histogram 0

Value

histogram

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.

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)