histWSAF: WSAF histogram

In DEploid.utils: 'DEploid' Data Analysis and Results Interpretation

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)

DEploid.utils documentation built on April 3, 2025, 9:58 p.m.