getMAF: Get minor-allele-frequency

In kullrich/vGWAS: Variance Heterogeneity Genome-wide Association Study - Reimplementation

Get minor-allele-frequency

Description

Calculates minor-allele-frequency (MAF)

Usage

getMAF(geno.matrix, geno.snp = "row", include.het = FALSE)

Arguments

geno.matrix	a matrix or data.frame or sparseMatrix with individuals as columns and markers as rows (geno.snp = "row") or individuals as rows and markers as columns (geno.snp = "col").
geno.snp	if individuals at columns and markers at rows use "row" else if individuals at rows and markers at columns use "col"
include.het	specify if heterozygous calls should be split and added equally to homozygous ref and alt counts (default = FALSE)

Value

a vector containing minor-allele-frequency values

Author(s)

Kristian Ullrich

Examples

data(geno)
maf <- getMAF(geno.matrix = geno, geno.snp = "col")
data(geno.num)
maf.num <- getMAF(geno.matrix = geno.num, geno.snp = "col")
data(geno.df)
maf.df <- getMAF(geno.matrix = geno.df, geno.snp = "row")
data(geno.sparse)
maf.sparse <- getMAF(geno.matrix = geno.sparse, geno.snp = "row")

kullrich/vGWAS documentation built on June 10, 2025, 3:56 a.m.