R/get_genotypes_from_pgen.R

In Lab-Jaiswal/tools4ukbb: What the Package Does (One Line, Title Case)

#' A tools4ukbb function
#' Function output: grouped datframe to be used in get_genotype. Do not use this function alone except for unit testing.
#'
#' @param variants a list of variants you are interested in
#' @param variants_df dataframe with 3 columns: variant names, their chromosome, and their index
#' @param pgen_list list of pgens generated from get_pgen_list
#' @keywords get_genotypes_from_pgen
#' @export
#' @examples
#' get_genotypes_from_pgen()

get_genotypes_from_pgen <- function(variants, variants_df, pgen_list) {
  chr_name <- unique(variants_df$chromosome)
  print(chr_name)
  pgen_handle <- pgen_list[[chr_name]]
  geno_mat <- ReadList(pgen_handle, variants$index, meanimpute=F)
  colnames(geno_mat) <- variants$variant_id
  geno_mat
}