makehaplist: Make list of sire haplotypes

In hsrecombi: Estimation of Recombination Rate and Maternal LD in Half-Sibs

Make list of sire haplotypes

Description

List of sire haplotypes is set up in the format required for hsrecombi. Haplotypes (obtained by external software) are provided.

Usage

makehaplist(daughterSire, hapSire, nmin = 1)

Arguments

daughterSire	vector (LEN n) of sire ID for each progeny
hapSire	matrix (DIM 2N x p + 1) of sire haplotype at p SNPs; 2 lines per sire, 1. columns contains sire ID
nmin	scalar, minimum number of progeny required, default 1

Value

list (LEN 2) of lists. For each sire:

famID

list (LEN N) of vectors (LEN n.progeny) of progeny indices relating to lines in genotype matrix

sireHap

list (LEN N) of matrices (DIM 2 x p) of sire haplotypes (0, 1) on investigated chromosome

Examples

  data(targetregion)
  hap <- makehaplist(daughterSire, hapSire)

hsrecombi documentation built on June 7, 2023, 6:02 p.m.