hh: Heatmap of Half-sibs

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

Heatmap of Half-sibs

Description

Creates a heatmap of a half-sib dataset using an opposing-homozygotes (OH) matrix, with optional sidebars showing inferred and/or real pedigree groupings.

Usage

hh(oh, inferredPedigree, realPedigree, pedOnly = TRUE)

Arguments

oh	matrix. Opposing-homozygotes matrix (e.g. output of ohg).
inferredPedigree	matrix. Inferred pedigree (e.g. output of rpoh).
realPedigree	matrix. Original pedigree.
pedOnly	logical. If TRUE, consider only individuals that exist in the real pedigree.

Value

Returns a heatmap of the OH matrix with sidebars color-coded by sire groups from the inferred and original pedigrees (where provided).

Author(s)

The function uses colors generated by the getcol function in the made4 package (Aedin Culhane).

See Also

ohg and rpoh

Examples

c1h1 <- .simulateHalfsib(numInd = 62, numSNP = 5000)
c1h2 <- .simulateHalfsib(numInd = 38, numSNP = 5000)
Genotype <- rbind(c1h1, c1h2)

oh <- ohg(Genotype)
hh(oh)

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