getmaf: Calculate minor allele frequency

Description Usage Arguments Value Examples

View source: R/WriteBinaryDosage.R

Description

Routine to calculate the minor allele frequency given the dosages. Missing values for dosage ignored. This function is used internally and is exported for use in examples. Note: The minor allele in one data set may be different from another data set. This can make comparing minor allele frequencies between data sets nonsensical.

Usage

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getmaf(dosage, p0, p1, p2)

Arguments

dosage

Dosage values

p0

Pr(g=0) - unused

p1

Pr(g=1) - unused

p2

Pr(g=2) - unused

Value

Minor allele frequency

Examples

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

BinaryDosage documentation built on Jan. 13, 2020, 5:06 p.m.