makehaplist {hsrecombi}

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)