Reconstructs a half-sib pedigree based on a matrix of opposing homozygotes.
rpoh(genotypeMatrix, oh, forwardVectorSize = 30, excludeFP = TRUE, nsap = 3,
maxRec = 15, intercept = 26.3415, coefficient = 77.3171, snpnooh, method, maxsnpnooh)Returns a data frame with two columns, the first column is animals' ID and the second column is sire identifiers (randomly generated).
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)
integer Opposing homozygotes matrix (Output of ohg)
integer number of heterozygous sites used to validate recombination events or check for genotyping errors
logical excludes SNPs that may cause heterozygous sites in the sire due to genotyping errors or map errors
integer number of SNP per block to validate recombinations
integer maximum number of expected recombinations per individual
integer intercept of fitted model
integer coefficient of fitted model
integer number of SNPs used to create oh matrix (this number must be divided by 1000)
character pedigree reconstruction method
numeric the maximum number of allowing opposing homozygote in a half-sib family
Four methods simple, recombinations, calus and manual can be
utilized to reconstruct the pedigree.
The following examples show the arguments require for each method.
pedigree1 <- rpoh(oh = oh, snpnooh = 732, method = "simple")
pedigree2 <- rpoh(genotypeMatrix = genotypeChr1, oh = ohg(genotype), maxRec = 10 , method = "recombinations")
pedigree3 <- rpoh(genotypeMatrix = genotype, oh = oh, method = "calus")
pedigree4 <- rpoh(oh = oh, maxsnpnooh = 31662, method = "manual")
bmh and recombinations