getaaf {BinaryDosage}

R Documentation

Calculate alternate allele frequency

Description

Routine to calculate the alternate allele frequency given the dosages. Missing values for dosage ignored. This function is used internally and is exported for use in examples.

Usage

getaaf(dosage, p0, p1, p2)

Arguments

dosage	Dosage values
p0	Pr(g=0) - unused
p1	Pr(g=1) - unused
p2	Pr(g=2) - unused

Value

Alternate allele frequency

Examples

# Get information about binary dosage file
bdfile <- system.file("extdata", "vcf1a.bdose", package = "BinaryDosage")
bdinfo <- getbdinfo(bdfiles = bdfile)
snp1 <- getsnp(bdinfo = bdinfo, 1)
aaf <- getaaf(snp1$dosage)

---