phase_parent: 'Phasing haplotypes of focal parent'

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

Description

Phasing focal parent's haplotypes using parents' genotypic data and progeny array's genotypic data. Parents' genotypic data can be either confident genotyping data, i.e., WGS data, or imputed genotypic data generated by impute_parent. This function was composed of two major parts: phase_chunk and join_chunks. The haplotype was phased using a sliding window and extended to a large chunk of sequence. The chunks were then joined into chromosomal wide haplotypes.

Usage

phase_parent(GBS.array, win_length = 10, join_length = 10, verbose = TRUE,
  OR = log(3))

output_phase(outchunks, info)

phase_error_rate(GBS.array, phase)

Arguments

GBS.array	A GBS.array object generated from impute_parent or sim.array functions. The slot gbs_parents replaced with imputed parental genotypes.
win_length	Window length used for halotype phasing. Default=10. win_length > 20 will dramatically increase computational burden.
join_length	The length of each neighboring chunks used to connect them into a longer one.
verbose	Writing verbose messages. Default=TRUE.

Value

return a data.frame with all the log likelihoods. Using function momgeno to extract mom's genotype.

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

Examples

GBS.array <- sim.array(size.array=50, numloci=1000, imiss=0.2, selfing=0.5)

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