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Set the ploidy of a gen_tibble to include pseudohaploids

Source: R/gt_pseudohaploid.R
gt_pseudohaploid.Rd

The ploidy of a gen_tibble 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.

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 <- 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