computeObsWSAF: Compute observed WSAF

In DEploid: Deconvolute Mixed Genomes with Unknown Proportions

Description

Compute observed allele frequency within sample from the allele counts.

Usage

computeObsWSAF(alt, ref)

Arguments

alt	Numeric array of alternative allele count.
ref	Numeric array of reference allele count.

Value

Numeric array of observed allele frequency within sample.

See Also

histWSAF for histogram.

Examples

# Example 1
refFile = system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
altFile = system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
PG0390CoverageT = extractCoverageFromTxt(refFile, altFile)
obsWSAF = computeObsWSAF(PG0390CoverageT$altCount, PG0390CoverageT$refCount)

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

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