Islands of runs of homozygosity

Finds the regions of the genome where many individuals (at least a proportion threshold of them, overall or in each group) are in runs of homozygosity: islands of runs of homozygosity (also called ROH hotspots), which can point to regions under selection.

Usage

gt_roh_islands(roh, loci, threshold = 0.5, 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)

threshold

the smallest proportion of individuals in a run for a locus to be in an island (default 0.5)

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 island, with the grouping variables (if counting by group), chromosome, start and end (the positions of its first and last loci), length_bp (end - start + 1), n_loci, first_locus and last_locus (rows of the loci table), and max_prop and mean_prop (the largest and mean proportions of individuals in a run over its loci)

Details

Islands are stretches of consecutive loci of a chromosome that are in runs in at least threshold of the individuals (see gt_roh_loci()).

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))
# regions in runs in at least 20% of the individuals of a population
gt_roh_islands(sim_roh, show_loci(sim_gt), threshold = 0.2)
#> # A tibble: 8 × 10
#>   group    chromosome   start     end length_bp n_loci first_locus last_locus
#>   <chr>    <fct>        <int>   <int>     <int>  <int>       <int>      <int>
#> 1 inbred   1          1714516 8848406   7133891    724         165        888
#> 2 inbred   2          4700515 7489836   2789322    424        1507       1930
#> 3 inbred   3           754836 5045384   4290549    732        2131       2862
#> 4 moderate 1          2355826 4160156   1804331    179         227        405
#> 5 moderate 2          5845283 6269528    424246     67        1682       1748
#> 6 moderate 3          1495251 1802415    307165     59        2244       2302
#> 7 moderate 3          2703613 3009866    306254     63        2456       2518
#> 8 moderate 3          3763235 4112239    349005     53        2641       2693
#> # ℹ 2 more variables: max_prop <dbl>, mean_prop <dbl>