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

The hh function creates a heatmap of the half-sib families using the matrix of opposing homozygotes.

Usage

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

Arguments

oh	matrix Opposing homozygotes matrix (output of ohg)
inferredPedigree	matrix inferred pedigree (output of rpoh)
realPedigree	matrix original pedigree
pedOnly	logical Consider only individuals that are exist in the real pedigree

Value

Returns the heatmap of the matrix of opposing homozygotes with sidebars colour coded by sires from the inferred and original pedigree.

Author(s)

The fuction uses the colour generated by 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) # creating the Opposing Homozygote matrix
hh(oh)

hsphase documentation built on May 29, 2024, 2:20 a.m.