read.Happyinf.output: read the haplotyping results from the Happy-inf output

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

Description

read the haplotyping results from the Happy-inf output

Usage

read.Happyinf.output(file_prefix, dropUnused=TRUE)

Arguments

file_prefix	the prefix for the output files generated by Happy-inf (the value of the -o parameter)
dropUnused	TRUE (default) if the returned matrix should only contain rows for haplotypes that are present; if FALSE matrix contains rows for all possible haplotypes

Details

This function reads the <file_prefix>.stat.dat and <file_prefix>.stats.dat files. The first contains one row per SNP marker, grouped per haploblock and <ploidy> columns per individual with the SNP haplotypes, where SNP alleles are represented as 0 or 1, or NA for unknown. For one SNP, the <ploidy> alleles in an individual are all known or all unknown It is possible that of the different SNPs in a haploblock some are known and some are not; in the conversion to PolyHaplotyper format all these partially known haplotypes are made unknown. The latter file has a statistics "mismatch" and "ratio" for each individual / haploblock combination; for their meaning see the Happyinf readme file.

Value

a list with 2 items:
$hapdos is a matrix with individuals in columns and haplotypes in rows, giving the dosages of the haplotypes in each individual (summing to ploidy). This is the same format as the hapdos components of the inferHaplotypes results of PolyHaplotyper except that
$stats is a matrix with individuals in rows (matching dosmat) and two rows named mismatch and ratio.

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