impute_kid: 'Phasing and Imputing Kid Genotypes'

In yangjl/imputeR: Imputation of GBS genotypes via window phasing

Description

Calculate the maximum likelihood of the inherited haplotypes. And then find the minimum path of recombinations. At the potential recombination sites, find the maximum likelihood of the breaking points.

Usage

impute_kid(geno, pp, ped, verbose = TRUE)

one_kid_hap(pp1, pp2, subgeno_all)

hap_in_chunk(p1, p2, c, subgeno)

which_kid_hap(p1_haps, p2_haps, kidwin)

Arguments

verbose	Writing verbose messages. Default=TRUE.
p1_haps	Two haplotypes in a chunk of the first parent.
p2_haps	All possible haplotypes in chunks of the 2nd parent.
kidwin	The genotypes of the kid for all heterozygote site of both parents.
GBS.array	A GBS.array object with phased parents. It can be generated from phase_parent orsim.array functions.
winsize	The size of window for determining kid haplotype. Default=100.

Value

return GBS.array object with kid hapltoypes in slot gbs_kids.

See https://github.com/yangjl/imputeR/blob/master/vignettes/imputeR-vignette.pdf for more details.

Examples

set.seed(123457)
GBS.array <- sim.array(size.array=50, numloci=10000, hom.error = 0.02, het.error = 0.8,
                       rec = 0.25, selfing = 0.5, imiss = 0.5, misscode = 3)
#get perfectly phased parents
GBS.array <- get_phased(GBS.array, maxchunk=3)
#get probability matrices
probs <- error_mx(hom.error=0.02, het.error=0.8, imiss=0.5) 
phased <- impute_kid(GBS.array, winsize=10, verbose=TRUE)

yangjl/imputeR documentation built on May 4, 2019, 2:28 p.m.