histWSAF {DEploid}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")
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)


[Package DEploid version 0.5.4 Index]