genotype.loci: Genotype loci

In UMN-BarleyOatSilphium/GSSimTPUpdate: Code and data to accompany the publication [TITLE]

Description

Creates a loci design matrix given a haploid matrix or a list of haploid matricies.

Usage

genotype.loci(haploid.genos, genome, include.QTL = FALSE, error.rate = 0,
  missing.prop = 0)

Arguments

haploid.genos	A 2n x m matrix of haploid alleles at m loci for n individuals.
genome	The hypred genome.
include.QTL	Logical whether to include the QTL in the design matrix. Default is FALSE.
error.rate	The rate of genotyping errors for a particular individual. Used to draw from a binomial distribution whether to introduce error. The conversion of a heterozygous genotype to one of the homozygotes or from a homozygous genotype to a heterozygote or one of the homozygotes will occur will equal probability.
missing.prop	The proportion of missing data across the genotype calls. Genotype calls are randomly assigned missing to obtain the desired missingness proportion.

UMN-BarleyOatSilphium/GSSimTPUpdate documentation built on May 9, 2019, 7:40 p.m.