makehappm: Make list of imputed haplotypes and recombination rate

Description Usage Arguments Value References Examples

View source: R/functions.R

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

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

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 on a single chromosome with p SNPs

nmin

scalar, minimum number of progeny required, default 1

Value

hap 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

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

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hsrecombi documentation built on March 23, 2021, 9:07 a.m.