Set the ploidy of a gen_tibble to include pseudohaploids

If a gen_tibble includes pseudohaploid data, its ploidy is set to -2 to indicate that some individuals are coded as pseudohaploids. The ploidy of the individuals is updated, with pseudohaploids set to 1 and diploids set to 2. However, the dosages are not changed, meaning that pseudohaploids are still coded as 0 or 2. If the gen_tibble is already set to pseudohaploid, running gt_pseudohaploid will update the ploidy values again, if pseudohaploid individuals have been removed then ploidy is reset to 2.

Usage

gt_pseudohaploid(x, test_n_loci = 10000)

Arguments

x: a gen_tibble object
test_n_loci: the number of loci to test to determine if an individual is pseudohaploid. If there are no heterozygotes in the first test_n_loci loci, the individual is considered a pseudohaploid. If NULL, all loci are tested.

Value

a gen_tibble object with the ploidy set to -2 and the individual ploidy values updated to 1 or 2.

Examples

example_gt <- load_example_gt("gen_tbl")

# Detect pseudohaploids and set ploidy for the whole gen_tibble
example_gt <- example_gt %>% gt_pseudohaploid(test_n_loci = 3)

# Ploidy is now set to -2
show_ploidy(example_gt)
#> [1] -2

# Individual ploidy now varies between 1 (pseudohaploid) and 2 (diploid)
indiv_ploidy(example_gt)
#> [1] 2 2 1 2 2 1 2