computeObsWSAF {DEploid.utils}R Documentation

Compute observed WSAF

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.utils")
altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid.utils")
PG0390CoverageTxt <- extractCoverageFromTxt(refFile, altFile)
obsWSAF <- computeObsWSAF(PG0390CoverageTxt$altCount, PG0390CoverageTxt$refCount)

# 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)


[Package DEploid.utils version 0.0.1 Index]