check_ploidy: Check ploidy for tetraploids
In jendelman/polyBreedR: Genomics-assisted breeding for polyploids (and diploids)

check_ploidy

R Documentation

Check ploidy for tetraploids

Description

Fraction of simplex or triplex markers

Usage

check_ploidy(geno = NULL, map = NULL, vcf.file = NULL, max.missing = 0.1)

Arguments

`geno`	Genotype matrix (markers x indiv)
`map`	Data frame with marker map (Marker, Chrom, Position)
`vcf.file`	VCF file input
`max.missing`	maximum proportion of missing data allowed per marker

Details

For every indiv in the genotype matrix, the fraction of markers per chromosome called as simplex or triplex is calculated, which should be low for diploids. A small amount of missing genotype data can be tolerated.

As of v4.2, a VCF file can be used as input instead