ohplot: Opposing Homozygotes Plot

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

Opposing Homozygotes Plot

Description

Plot the sorted vectorized matrix of Opposing Homozygotes.

Usage

ohplot(oh, genotype, pedigree, check = FALSE)

Arguments

oh	integer Opposing homozygotes matrix (Output of ohg)
genotype	matrix genotype of one chromosome (data should be numeric. Use 0, 1 and 2 for respectively AA, AB and BB. Use 9 for missing data)
pedigree	matrix the pedigree matrix should contain at least two columns, the first column with the half-sib IDs and the second column with the sires IDs. This argument is optional.
check	logical check the genotype file for the possible errors

Details

The cut off line shows the edge of most different groups.

See Also

ohg and rpoh

Examples

set.seed(100)
chr <- list()
sire <- list()
set.seed(1)
chr <- list()
for(i in 1:5)
{
	chr[[i]] <- .simulateHalfsib(numInd = 20, numSNP = 5000, recbound = 1:10)
	sire[[i]] <- ssp(bmh(chr[[i]]), chr[[i]])
	sire[[i]] <- sire[[i]][1,] + sire[[i]][2,]
	sire[[i]][sire[[i]] == 18] <- 9
}

Genotype <- do.call(rbind, chr)
rownames(Genotype) <- 6:(nrow(Genotype) + 5)
sire <- do.call(rbind, sire)
rownames(sire) <- 1:5
Genotype <- rbind(sire, Genotype)
oh <- ohg(Genotype)  # creating the Opposing Homozygote matrix
pedigree <- as.matrix(data.frame(c(1:5, 6:(nrow(Genotype))), 
rep = c(rep(0,5), rep(1:5, rep(20,5)))))
ohplot(oh, Genotype, pedigree, check = TRUE)

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