join_chunks: 'Joining phased haplotype chunks. '

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

Description

Extending/joining the phased haplotype chunks generated from phase_chunk.

Usage

join_chunks(GBS.array, chunklist, join_length, verbose, OR)

link_dad_haps(GBS.array, dad_haps_lofl, hapidx, join_length, OR)

Arguments

GBS.array	A GBS.array object generated from impute_parent orsim.array functions.
chunklist	A list of haplotype chunks generated from phase_chunk.
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 list of haplotype chunks.

Examples

GBS.array <- sim.array(size.array=50, numloci=1000)
win_length = 10
haps <- setup_haps(win_length)
probs <- error_mx(hom.error=0.02, het.error=0.8, imiss=0.2) 
chunklist <- phase_chunk(GBS.array, win_length, haps, verbose=TRUE)
res <- join_chunks(GBS.array, chunklist, join_length, verbose=TRUE)

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