usedhap: Find all used (inferred) haplotypes

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

Description

Find all haplotypes for a haploblock that were inferred to be present in the population (i.e. all haplotypes used for haplotyping any of the individuals)

Usage

usedhap(hapresults, haploblock)

Arguments

hapresults	list as returned by inferhaplotypes, or one element of such a list (i.e. the results for one haploblock)
haploblock	if hapresults is one element of the return value of inferHaplotypes, haploblock should be missing of NULL; else haploblock is a single value indicating the haploblock: either its name of its index in hapresults

Details

This function works with the results of inferHaplotypes; the setting of dropUnused does not affect this function

Value

an array with the haplotypes that are used in the population. The haplotypes are in columns, with the haplotype numbers as colnames; the markers are in rows.

Examples

data(PolyHaplotyper_small)
# show the composition of haplotypes inferred to be present
# in the first haploblock:
usedhap(hapresults=phresults, haploblock=1)

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