getmaf: Calculate minor allele frequency

In BinaryDosage: Creates, Merges, and Reads Binary Dosage Files

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

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

# 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.