madc: Multi-Allelic Haplotype Counts for potato DArTag

In jendelman/polyBreedR: Genomics-assisted breeding for polyploids (and diploids)

Multi-Allelic Haplotype Counts for potato DArTag

Description

Multi-Allelic Haplotype Counts for potato DArTag

Usage

madc(madc.file, marker)

Arguments

madc.file	MADC filename
marker	Name of marker ("CDF1","OFP20")

Details

Due to multi-allelism, for some trait markers a correct interpretation is not possible using the collapsed counts file; the MADC (Missing Allele Discovery Count) file is needed.

"CDF1" uses marker CDF1.4_chr05_4488021 to detect the 2C, 2T, and 4 alleles; all other haplotypes are treated as allele 1. Allele 3 is not detected by the assay.

"OFP20" relies on three markers. Marker OFP20_M6_CDS_994 detects OFP20.1 as Alt and most other haplotypes as Ref, but some alleles appear to be NULL. Marker OFP20_M6_CDS_171 detects allele 2 as Alt and alleles 3 and 7 as Ref; other alleles are NULL. Marker OFP20_M6_CDS_24 detects allele 8 as Ref and most other alleles as Alt. Given the high allelic diversity at this locus, this function may not work in all germplasm groups.

Value

matrix of haplotype counts

jendelman/polyBreedR documentation built on Jan. 5, 2025, 12:13 a.m.