build_MBP: Build reference panel for MBP (MC1R-based breed probability)...

In funkhou9/breedTools: Tools for use in breed composition prediction using genomic data

Description

MBP (MC1R-based breed probabilities) utilize a reference panel of purebred animals' genotypes. The genotypes are phased, and the resulting haplotypes are used to construct haplotype frequences, genotype frequencies given breed P(g | b), and finally breed probabilities given a genotype P(b | g). This method is used to construct a reference panel of breed probabilities for which one can use to test the probability that an animal is of a certain breed, in the region of MC1R.

Usage

build_MBP(geno, map, ped = NULL, path = NULL, groups = NULL,
  keep_fimpute = FALSE, parent = FALSE, reference = FALSE)

Arguments

geno	a matrix or data.frame with genotypes of reference animals. SNPs in columns and individuals in rows. Genotypes must be coded as dosage of allele 'b' 0, 1, 2.
map	a data.frame containing SNP map information for each SNP present in geno
ped	a data.frame pedigree providing family information for each individual in geno. The first column of the pedigree is for ID, second is for sire/father ID, third is for dam/mother ID, fourth is sex of ID "M" or "F". If ids in geno are not present in pedigree, they will be added to the end with missing parent information and a "M" sex. Correct sex information should only be required when imputing/phasing the sex chromosomes.
path	a character represting the path to the FImpute binary. If omitted, assumes FImpute binary resides along PATH.
groups	a list of character vectors with the names of IDs meant to be processed as groups. Names of list should be the names of the groups, with each element containing IDs.
keep_fimpute	logical if TRUE, output files generated from snpTools::fimpute_run are kept. By default, build_KBP will use fimpute_run to build haplotypes, but as soon as haplotypes are extracted, fimpute output will be deleted so not to clutter hard drive space.
parent	logical if TRUE, breed probabilities or haplotypes will be returned only from parents and not from progeny,
reference	logical use TRUE if you want 'groups' to be used to specify the reference animals used by FImpute. Not compatable with parent TRUE.

Value

a data.frame containing breed probabilities for each genotype made possible from the reference animal haplotypes

funkhou9/breedTools documentation built on May 16, 2019, 4:04 p.m.