groupMatSingle: Grouping a Half-sib Family

In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

Grouping a Half-sib Family

Description

Group the genotype or haplotype of a half-sib family into partitions using opposing homozygotes.

Usage

groupMatSingle(haplotype, windowsSize, cpus = 2, input = "haplotype", oh = 0)

Arguments

haplotype	matrix. Haplotypes (two rows per individual) or genotypes (one row per individual) depending on input.
windowsSize	integer. Partition size.
cpus	integer. Number of CPU threads.
input	character. Either "haplotype" or "genotype".
oh	integer. Threshold for opposing homozygotes used for grouping (increase if genotyping errors exist).

Value

A grouping matrix.

See Also

addSwitch and fixSW

Examples

haplotype <- .simulateHalfsib(10, 5000, type = "haplotype")$phased
gMat <- groupMatSingle(haplotype, 100, 2, "haplotype")
imageplot(gMat)

hsphase documentation built on Feb. 17, 2026, 5:07 p.m.