solve_MBP: Solve MC1R-Based Breed Probabilities (MBP)

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

Description

Given a breed probability matrix (provided by build_MBP()), and a set of test animals genotypes, use this function to derive breed probabilities for each test animal genotype based on 8 SNPs within a 2MB window around the MC1R gene.

Usage

solve_MBP(geno, b_mat, white = FALSE)

Arguments

geno	a matrix or data.frame with genotypes of test animals. SNPs in columns and individuals in rows. Genotypes must be coded as dosage of allele 'b' 0, 1, 2. NOTE, only 8 SNPs surrounding MC1R will actually be used.
b_mat	a data.frame that contains genotypes in rows and associated breed probabilities in columns. This is the output of build_MBP().
white	a logical indicating whether "white" breeds (Yorkshire and Landrace, assuming present) should be grouped together into a white breed probability. For MC1R analysis, this is set to FALSE by default.

Value

a data.frame containing test animals in rows and KBPs in columns

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