Convert a gen_tibble to a genind object from adegenet

This function converts a gen_tibble to a genind object from adegenet. genind objects support arbitrary ploidy (including mixed-ploidy data across individuals), so this works on diploid, polyploid and mixed-ploidy gen_tibble objects alike.

Usage

gt_as_genind(x)

Arguments

x

a gen_tibble, with population coded as 'population'

Value

a genind object

Note

pseudohaploid individuals are treated as diploid (ploidy 2) using their stored genotype counts (dosage 0/2) directly, the same convention used by other tools (e.g. PLINK) when handling pseudohaploid data.

Examples

example_gt <- load_example_gt("gen_tbl")

# Convert to genind
gt_genind <- example_gt %>% gt_as_genind()

# Check object class
class(gt_genind)
#> [1] "genind"
#> attr(,"package")
#> [1] "adegenet"