R/gt_as_genind.R

In tidypopgen: Tidy Population Genetics

#' Convert a `gen_tibble` to a `genind` object from `adegenet`
#'
#' This function converts a `gen_tibble` to a `genind` object from `adegenet`
#'
#' @param x a [`gen_tibble`], with population coded as 'population'
#' @returns a `genind` object
#' @export
#' @examplesIf rlang::is_installed("adegenet")
#' example_gt <- load_example_gt("gen_tbl")
#'
#' # Convert to genind
#' gt_genind <- example_gt %>% gt_as_genind()
#'
#' # Check object class
#' class(gt_genind)
gt_as_genind <- function(x) {
  if (!requireNamespace("adegenet", quietly = TRUE)) {
    stop(
      "to use this function, first install package 'adegenet' with\n",
      "install.packages('adegenet')"
    )
  }
  df_for_genind <- show_genotypes(x)
  df_for_genind[df_for_genind == 0] <- "11"
  df_for_genind[df_for_genind == 1] <- "12"
  df_for_genind[df_for_genind == 2] <- "22"
  adegenet::df2genind(
    X = df_for_genind,
    ind.names = x$id,
    pop = x$population,
    ncode = 1,
    loc.names = loci_names(x)
  )
}