build_local_reference: Build reference panel of breed probabilities

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

Description

Generalized function to build a reference panel, used to estimate breed probabilities for a set of multi-locus genotypes from a specified region.

Usage

build_local_reference(chr, markers, geno_, map_, ped_ = NULL, path_ = NULL,
  groups_ = NULL, keep_fimpute_ = FALSE, parent_ = FALSE,
  reference_ = FALSE)

Arguments

chr	character providing the chromosome requiring phasing
markers	character vector containing names of probes used to construct multi-locus haplotypes
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.