compareHapresults: compare two haplotyping results

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

Description

compare two haplotyping results, e.g. PolyHaplotyper and SATlotyper

Usage

compareHapresults(haploblock, hapresultsA, hapresultsB)

Arguments

haploblock	a list of character vectors. The names are the names of the haploblocks, the character vectors have the names of the markers in each haploblock.
hapresultsA	and
hapresultsB	two 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 haploblocks in param haploblock must occur in hapresultsA and in hapresultsB. The individual names (colnames of the hapdos items for each haploblock) must be identical and in the same order in hapresultsA and hapresultsB

Value

a list with one element per haploblock in param haploblock. Each element is itself a list with elements: $identical: TRUE or FALSE
$message: a single string, "" if the comparison is possible, else the reason why not (if $message is not "", $identical is always FALSE). The next elements are only present if $message is "":
$compindiv: a matrix comparing the two hapdos, with one column per individual and 5 rows: Both_NA, A_NA, B_NA, Equal, Uneq. The last 2 have NA values if A and/or B is NA $haplofreq: a matrix with one row per haplotype occurring in A and/or B, and columns A and B, with the total frequency of each haplotype in hapdos A or hapdos B

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