solve_composition: Compute genome-wide breed composition

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

Description

Computes genome-wide breed/ancestry composition using quadratic programming on a batch of animals.

Usage

solve_composition(Y, X, ped = NULL, groups = NULL, mia = FALSE,
  sire = FALSE, dam = FALSE)

Arguments

Y	numeric matrix of genotypes (columns) from all animals (rows) in population coded as dosage of allele B 0, 1, 2
X	numeric matrix of allele frequencies (rows) from each reference panel (columns). Frequencies are relative to allele B.
ped	data.frame giving pedigree information. Must be formatted "ID", "Sire", "Dam"
groups	list of IDs catagoriezed by breed/population. If specified, output will be a list of results categorized by breed/population.
mia	logical. Only applies if ped argument is supplied. If true, returns a data.frame containing the inferred maternally inherited allele for each locus for each animal instead of breed composition results.
sire	logical. Only applies if ped argument is supplied. If true, returns a data.frame containing sire genotypes for each locus for each animal instead of breed composition results.
dam	logical. Only applies if ped argument is supplied. If true, returns a data.frame containing dam genotypes for each locus for each animal instead of breed composition results.

Value

A data.frame or list of data.frames (if groups is !NULL) with breed/ancestry compostion results

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