makehappm {hsrecombi}

Make list of imputed haplotypes and estimate recombination rate

Description

List of sire haplotypes is set up in the format required for hsrecombi. Sire haplotypes are imputed from progeny genotypes using R package hsphase. Furthermore, recombination rate estimates between adjacent SNPs from hsphase are reported.

Usage

makehappm(sireID, daughterSire, genotype.chr, nmin = 30, exclude = NULL)

Arguments

sireID

vector (LEN N) of IDs of all sires

daughterSire

vector (LEN n) of sire ID for each progeny

genotype.chr

matrix (DIM n x p) of progeny genotypes (0, 1, 2) on a single chromosome with p SNPs; 9 indicates missing genotype

nmin

scalar, minimum required number of progeny for proper imputation, default 30

exclude

vector (LEN < p) of SNP IDs (for filtering column names of genotype.chr) to be excluded from analysis

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

probRec

vector (LEN p - 1) of proportion of recombinant progeny over all families between adjacent SNPs

numberRec

list (LEN N) of vectors (LEN n.progeny) of number of recombination events per animal

gen

vector (LEN p) of genetic positions of SNPs (in cM)

References

Ferdosi, M., Kinghorn, B., van der Werf, J., Lee, S. & Gondro, C. (2014) hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups BMC Bioinformatics 15:172. https://CRAN.R-project.org/package=hsphase

Examples

  data(targetregion)
  hap <- makehappm(unique(daughterSire), daughterSire, genotype.chr, exclude = paste0('V', 301:310))