Description Usage Arguments Value See Also Examples
Compute observed allele frequency within sample from the allele counts.
1 | computeObsWSAF(alt, ref)
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alt |
Numeric array of alternative allele count. |
ref |
Numeric array of reference allele count. |
Numeric array of observed allele frequency within sample.
histWSAF
for histogram.
1 2 3 4 5 6 7 8 9 10 | # 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)
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