The loci in runs of homozygosity

Counts, for each locus, the individuals that are in a run of homozygosity (as found by windows_indiv_roh()), overall or in each group. Loci that are in runs in most individuals of a population (see gt_roh_islands()) can point to regions under selection. The counts are those of the .hom.summary file of PLINK --homozyg.

Usage

gt_roh_loci(roh, loci, by_group = TRUE)

Arguments

roh

an indiv_roh object, as returned by windows_indiv_roh()

loci

the loci table of the gen_tibble used to find the runs (i.e. show_loci(x), as the runs refer to its rows)

by_group

if roh was found on a grouped gen_tibble, whether to count the individuals of each group (the default) or of all groups

Value

a tibble with one row per locus (and per group), with the grouping variables (if counting by group), name, chromosome, position, n_roh (the number of individuals in a run), n_indiv (the number of individuals) and prop_roh (n_roh / n_indiv)

See also

gt_roh_islands() to find the regions in runs in many individuals, and autoplot.indiv_roh() (type = "coverage") to plot them.

Examples

bed_file <- system.file("extdata", "roh", "roh_sim.bed",
  package = "tidypopgen"
)
sim_gt <- gen_tibble(bed_file, backingfile = tempfile(), quiet = TRUE)
sim_roh <- windows_indiv_roh(sim_gt %>% group_by(population))
roh_loci <- gt_roh_loci(sim_roh, show_loci(sim_gt))
# the loci most often in runs in each population
roh_loci %>%
  group_by(group) %>%
  slice_max(prop_roh, n = 1, with_ties = FALSE)
#> # A tibble: 3 × 7
#> # Groups:   group [3]
#>   group    name    chromosome position n_roh n_indiv prop_roh
#>   <chr>    <chr>   <fct>         <int> <int>   <int>    <dbl>
#> 1 inbred   snp2551 3           3230132     7      10      0.7
#> 2 moderate snp227  1           2355826     2      10      0.2
#> 3 outbred  snp1    1             24153     0      10      0