compareHapMrkDosages: compare haplotyping results with observed markers dosages

In PolyHaplotyper: Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids

Description

compare haplotyping results with observed markers dosages

Usage

compareHapMrkDosages(mrkDosage, hapresults)

Arguments

mrkDosage	a data.frame or matrix with the marker dosages, in the format of inferHaplotypes()
hapresults	a list as returned by inferHaplotypes, with one item (itself a list) per haploblock with at least a matrix hapdos and a character vector markers. All markers in all haploblocks must also occur in mrkDosages, and all individuals in the hapdos matrices must also occur in mrkDosages

Value

a 3-D array with dimensions haploblock, individual, and chkresult: mrkNA (ALL markers in the haploblock have missing data for the individual), hapNA (the haplotype dosages do not sum to ploidy and/or are missing), match (TRUE if the non-missing marker dosages match the haplotype dosages, FALSE is there is a conflict, NA if mrkNA and/or hapNA are TRUE) Each element is itself a list with elements:

Examples

data(PolyHaplotyper_small)
chmd <- compareHapMrkDosages(mrkDosage=phdos, hapresults=phresults)
# show results for first haploblock, first 8 individuals:
chmd[1, 1:8,]

PolyHaplotyper documentation built on June 17, 2021, 5:12 p.m.