histWSAF: WSAF histogram

In DEploid: Deconvolute Mixed Genomes with Unknown Proportions

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")
altFile = system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
PG0390Coverage = extractCoverageFromTxt(refFile, altFile)
obsWSAF = computeObsWSAF(PG0390Coverage$altCount, PG0390Coverage$refCount)
histWSAF(obsWSAF)
myhist = histWSAF(obsWSAF, FALSE)

# Example 2
vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
PG0390CoverageV = extractCoverageFromVcf(vcfFile)
obsWSAF = computeObsWSAF(PG0390CoverageV$altCount, PG0390CoverageV$refCount)
histWSAF(obsWSAF)
myhist = histWSAF(obsWSAF, FALSE)

DEploid documentation built on April 22, 2020, 1:04 a.m.