In yasmina-mekki/gwhap: Genome wide haplotype analysis

knitr::opts_chunk$set(echo = TRUE)

library(gwhap)

Example with package toy bgen

toy_bgen_fn <- system.file("extdata", "haplotypes.bgen",package="gwhap", mustWork=TRUE)
phased_dl.bgen = phased_data_loader.bgen(toy_bgen_fn)
# ranges = data.frame(chromosome = "1", start = 1, end = 10000)
# diploHaplo.bgen = getDiploHaplo(phased_dl.bgen, ranges=ranges)
# diploHaplo.bgen
samples_selected = c("sample_0","sample_1","sample_2","sample_3")
haplotypes.bgen = determine_haplotypes_per_bloc(phased_dl.bgen, chromosome="1", start=1, end=1000,
                                                   sample_iid=samples_selected,
                                                   sample_bgen_iid_code=samples_selected)
haplotypes.bgen

Example with package toy haps

toy_hap_fn <- system.file("extdata", "haplotypes.haps" ,package="gwhap", mustWork=TRUE)
phased_dl.haps = phased_data_loader.haps(toy_hap_fn)
# diploHaplo.haps = getDiploHaplo(phased_dl.haps)
# diploHaplo.haps
samples_selected = c("sample_0","sample_1","sample_2","sample_3")
haplotypes.haps = determine_haplotypes_per_bloc(phased_dl.haps, chromosome="1", start=1, end=4,
                                                   sample_iid=samples_selected,
                                                   sample_bgen_iid_code=samples_selected)
haplotypes.haps

yasmina-mekki/gwhap documentation built on Dec. 31, 2021, 9:19 p.m.