guess_phase: Guess phase of imputed genotypes

Description

Turn imputed genotypes into phased genotypes along chromosomes by attempting to pick the phase that leads to the fewest recombination events.

Usage

guess_phase(cross, geno, deterministic = FALSE, cores = 1)

Value

If input cross is phase-known (e.g., recombinant inbred lines), the output will be the input geno. Otherwise, the output will be a list of three-dimensional arrays of imputed genotypes, individual x position x haplotype (1/2).

Arguments

cross: Object of class "cross2". For details, see the R/qtl2 developer guide.
geno: Imputed genotypes, as a list of matrices, as from maxmarg().
deterministic: If TRUE, preferentially put smaller allele first when there's uncertainty. If FALSE, the order of alleles is random in such cases.
cores: Number of CPU cores to use, for parallel calculations. (If 0, use parallel::detectCores().) Alternatively, this can be links to a set of cluster sockets, as produced by parallel::makeCluster().

Details

We randomly assign the pair of alleles at the first locus to two haplotypes, and then work left to right, assigning alleles to haplotypes one locus at a time seeking the fewest recombination events. The results are subject to arbitrary and random choices. For example, to the right of a homozygous region, either orientation is equally reasonable.

Examples

Run this code

iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
gmap <- insert_pseudomarkers(iron$gmap, step=1)
probs <- calc_genoprob(iron, gmap, error_prob=0.002)
imp_geno <- maxmarg(probs)
ph_geno <- guess_phase(iron, imp_geno)