Convert a gen_tibble to a data.frame compatible with hierfstat

This function converts a gen_tibble to a data.frame formatted to be used by hierfstat functions.

Usage

gt_as_hierfstat(x)

Arguments

x

a gen_tibble, with population coded as 'population'

Value

a data.frame with a column 'pop' and further column representing the genotypes (with alleles recoded as 1 and 2)

Note

hierfstat only supports haploid or diploid data, so this function only works on diploid (or pseudohaploid) gen_tibble objects. Pseudohaploid data is simply treated as regular diploid genotype counts (dosage 0/2), the same convention used by other tools (e.g. PLINK).

Examples

example_gt <- load_example_gt("gen_tbl")

# Convert to hierfstat format
gt_hierfstat <- example_gt %>% gt_as_hierfstat()

# Check object class
class(gt_hierfstat)
#> [1] "data.frame"