permuteAllelesInHaplosNum: Haplotypes

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Haplotypes

Description

Permute alleles in haplotypes. In the scrm package, haplotypes are made of 0's and 1's, the former indicating ancestral alleles and the latter derived alleles. However, when one wants to simulate realistic data, one often converts haplotypes into genotypes encoded as allele dose. At this step, one may not want to always count the number of copies of the derived allele. It hence is useful to permute alleles beforehand.

Usage

permuteAllelesInHaplosNum(haplos, snps.toperm, verbose = 0)

Arguments

haplos	list of haplotypes returned by scrm, each component of which corresponds to a matrix with haplotypes in rows and SNP in columns
snps.toperm	vector of SNP identifiers corresponding to the SNPs to which allele permutation will be performed (column names of haplos)
verbose	verbosity level (0/1)

Value

list of haplotypes

Author(s)

Timothee Flutre

See Also

simulCoalescent, segSites2allDoses, haplosAlleles2num

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.