getAlleleFrequencies: Compute allele frequencies from genotype data.

In PhenotypeSimulator: Flexible Phenotype Simulation from Different Genetic and Noise Models

Description

Compute allele frequencies from genotype data.

Usage

getAlleleFrequencies(snp)

Arguments

snp	[N x 1] Vector of length [N] samples with genotypes of a single bi-allelic genetic variant/SNP encoded as 0,1 and 2.

Value

Vector with ref (0-encoded) and alt (1-encoded) allele frequencies.

Examples

# create snp vector with minor allele frequency 0.3
snp <- rbinom(200, 2, 0.3)
allelefreq <- getAlleleFrequencies(snp)

PhenotypeSimulator documentation built on July 16, 2021, 5:06 p.m.