pogc: Parent Offspring Group Constructor

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

Description

Assign offsprings to the parents.

Usage

pogc(oh, genotypeError)

Arguments

oh	integer opposing homozygotes matrix (Output of ohg)
genotypeError	integer number of genotypeing error allowed in the oh matrix

Value

Return a data frame with two columns. The first column is the animal ID and the second column is the parent ID.

See Also

ohg, hss 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
pogc(oh, 5)

hsphase documentation built on May 2, 2019, 3:44 p.m.