screen_purity: Calculate both GWBC and KBP for a test animal

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

Description

GWBC (Genome-wide breed composition) and KBP (KIT-based breed probabilities) are calculations done together to assess the breed composition of a test animal and the probability that it is purebred in the KIT region of the genome, resposible for influencing color segregation patters. This function will assemble all GWBC and KBP results for any number of genotyped animals.

Usage

screen_purity(geno, gwbc_ref, kbp_ref, mbp_ref = NULL)

Arguments

geno	matrix containing genotyping data (dosage of allele B) for animals (in rows) for any number of SNPs (in columns)
gwbc_ref	data.frame containing allele frequencies for any number of SNPs (in rows) for any number of reference populations (in columns). See an example with 'data("GWBC_ref_A")'.
kbp_ref	data.frame containing genotype probabilities for various multi-locus genotypes surrounding the KIT region (the output of build_KBP).
mbp_ref	data.frame containing genotype probabilities for various multi-locus genotypes surrounding the MC1R region (the output of build_MBP). (OPTIONAL) If supplied, it will assume Hampshire animals are being evaluated in geno.

Value

data.frame with various GWBC and KBP values for each animal in geno

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