expandHapdos: Add dropped rows back to haplotype dosage matrix

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

Description

Haplotype dosage matrices generated with the dropUnused=TRUE lack some haplotypes that are required by pedigreeHapCheck; this function adds them back.

Usage

expandHapdos(hapdos, nhap, hbname)

Arguments

hapdos	a haplotype dosage matrix as returned by a.o. inferHaplotypes. The rownames are assumed to have all the same length: they are composed of the haploblock name to which the 0-padded haplotype number is appended, separated by "_"
nhap	the total number of haplotypes for the haploblock: nhap = 2^nmrk with nmrk the number of markers in the haploblock
hbname	the haploblock name (only used when hapdos has 0 rows)

Value

a matrix similar to hapdos with rows for the dropped haplotypes re-inserted, with the correct rownames and containing only 0 and NA values

Examples

# specify haplotype dosages of 4 tetraploid individuals,
# only the 3 occurring haplotypes (1, 5 and 6) are given:
haplodosg <- matrix(c(1,2,1, 4,0,0, 0,4,0, 0,0,4), nrow=3,
                   dimnames=list(paste0("demohap_", c(1,5,6)), paste0("indiv", 1:4)))
# add the rows for the absent haplotypes, assuming the haploblock consists
# of 3 markers, so 8 haplotypes are possible:
expandHapdos(hapdos=haplodosg, nhap=8)

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