Ifreqs: Compute allele frequencies from genotypes

In poolHelper: Simulates Pooled Sequencing Genetic Data

Compute allele frequencies from genotypes

Description

Computes alternative allele frequencies from genotypes by dividing the total number of alternative alleles by the total number of gene copies.

Usage

Ifreqs(nDip, genotypes)

Arguments

nDip	an integer representing the total number of diploid individuals to simulate. Note that scrm::scrm() actually simulates haplotypes, so the number of simulated haplotypes is double of this.
genotypes	a list of simulated genotypes, where each entry is a matrix corresponding to a different locus. At each matrix, each column is a different SNP and each row is a different individual.

Value

a list of allele frequencies. Each entry of the list corresponds to a different locus.

Examples

genotypes <- run_scrm(nDip = 10, nloci = 10)
Ifreqs(nDip = 10, genotypes)

poolHelper documentation built on July 9, 2023, 6:23 p.m.