get_parental_genotypes: get_parental_genotypes

In USDA-ARS-GBRU/crossword: Breeding program similation sotware

get_parental_genotypes

Description

The function collects the SNPs and their genotypes/gen2phy information for parental genotypes.

Usage

get_parental_genotypes(input,gen2phy,keep_homo)

Arguments

input	Required: a input vcf or hapmap file.
gen2phy	Required: gen2phy object, the output of "physical2genomic" function.
keep_homo	Optional: if TRUE only homozygous paretnal loci will be keept, otherwise the output will have homozygous and heterozygous parental loci

Value

A structured output of:
genotypes: the parental genotypes of SNPs.
gen2phy: the genetic loci of the SNPs

Examples

parental_genotypes = get_parental_genotypes('three_genotypes_snps.vcf',gen2phy,TRUE)

USDA-ARS-GBRU/crossword documentation built on April 5, 2023, 7:29 p.m.