Computes F_ROH, the proportion of the genome of each individual that is in
runs of homozygosity, from the runs found by windows_indiv_roh(). F_ROH
can be computed from the runs of at least a given length (e.g. 1, 2, 4, 8
and 16 Mb): long runs come from recent common ancestors, while short runs
also reflect older inbreeding.
Usage
gt_roh_froh(
roh,
min_length_mb = 0,
by = c("genome", "chromosome"),
genome_length = NULL
)Arguments
- roh
an
indiv_rohobject, as returned bywindows_indiv_roh()- min_length_mb
the smallest length of the runs to use, in Mb (default 0, i.e. all runs). With several values, F_ROH is computed for each.
- by
whether to compute F_ROH over the whole genome (
genome, the default), or for each chromosome (chromosome)- genome_length
the length of the genome, in bp (only used with
by = "genome"). Default is the sum of the lengths of the chromosomes (see Details).
Value
a tibble with one row per individual (including those with no
runs), with the grouping variables of roh (if any), id, the column
min_length_mb if there are several values, chromosome if by = "chromosome", length_bp (the total length of the runs) and froh.
Details
The length of the genome is, by default, the sum of the lengths of the
chromosomes, each being its largest position (as in detectRUNS); it can
be given instead with genome_length (e.g. the length of the autosomes of
the reference genome, or the length covered by the loci).
See also
autoplot.indiv_roh() to plot F_ROH.
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))
# F_ROH of each individual
gt_roh_froh(sim_roh)
#> # A tibble: 30 × 4
#> group id length_bp froh
#> <chr> <chr> <dbl> <dbl>
#> 1 outbred outbred_01 0 0
#> 2 outbred outbred_02 0 0
#> 3 outbred outbred_03 0 0
#> 4 outbred outbred_04 0 0
#> 5 outbred outbred_05 0 0
#> 6 outbred outbred_06 0 0
#> 7 outbred outbred_07 0 0
#> 8 outbred outbred_08 0 0
#> 9 outbred outbred_09 0 0
#> 10 outbred outbred_10 0 0
#> # ℹ 20 more rows
# from the runs of at least 1, 2 and 4 Mb
gt_roh_froh(sim_roh, min_length_mb = c(1, 2, 4))
#> # A tibble: 90 × 5
#> group id min_length_mb length_bp froh
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 outbred outbred_01 1 0 0
#> 2 outbred outbred_01 2 0 0
#> 3 outbred outbred_01 4 0 0
#> 4 outbred outbred_02 1 0 0
#> 5 outbred outbred_02 2 0 0
#> 6 outbred outbred_02 4 0 0
#> 7 outbred outbred_03 1 0 0
#> 8 outbred outbred_03 2 0 0
#> 9 outbred outbred_03 4 0 0
#> 10 outbred outbred_04 1 0 0
#> # ℹ 80 more rows
# on each chromosome
gt_roh_froh(sim_roh, by = "chromosome")
#> # A tibble: 90 × 5
#> group id chromosome length_bp froh
#> <chr> <chr> <fct> <dbl> <dbl>
#> 1 outbred outbred_01 1 0 0
#> 2 outbred outbred_01 2 0 0
#> 3 outbred outbred_01 3 0 0
#> 4 outbred outbred_02 1 0 0
#> 5 outbred outbred_02 2 0 0
#> 6 outbred outbred_02 3 0 0
#> 7 outbred outbred_03 1 0 0
#> 8 outbred outbred_03 2 0 0
#> 9 outbred outbred_03 3 0 0
#> 10 outbred outbred_04 1 0 0
#> # ℹ 80 more rows