ohplot {hsphase}

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)