R/GLstring_gene_copies_combine.R

In immunogenetr: A Comprehensive Toolkit for Clinical HLA Informatics

#' @title GLstring_gene_copies_combine
#'
#' @description A function for combining two columns of typing from the same
#' locus into a single column in the appropriate GL string format.
#'
#' @param .data A data frame
#' @param columns The names of the columns in the data frame that contain typing
#' information to be combined
#' @param sample_column The name of the column that identifies samples in the
#' data frame. Default is "sample".
#'
#' @return A data frame with the specified columns combined into a single column
#' for each locus, in GL string format.
#'
#' @examples
#' library(dplyr)
#' HLA_typing_1 %>%
#'   mutate(across(A1:B2, ~ HLA_prefix_add(.))) %>%
#'   GLstring_gene_copies_combine(c(A1:B2), sample_column = patient)
#'
#' @export
#'
#' @importFrom dplyr select
#' @importFrom dplyr mutate
#' @importFrom dplyr filter
#' @importFrom dplyr summarise
#' @importFrom dplyr rename_with
#' @importFrom dplyr %>%
#' @importFrom tidyr pivot_longer
#' @importFrom tidyr pivot_wider
#' @importFrom stringr str_extract
#' @importFrom stringr str_c
#' @importFrom stringr str_replace


GLstring_gene_copies_combine <- function(.data, columns, sample_column = "sample") {
  # Identify the columns to modify
  cols2mod <- names(select(.data, {{ columns }}))

  .data %>%
    pivot_longer(all_of(cols2mod), names_to = "locus", values_to = "allele") %>%
    mutate(locus = str_extract(allele, "HLA-[:alnum:]+")) %>%
    filter(!is.na(locus)) %>%
    summarise(allele = str_c(allele, collapse = "+"), .by = c({{ sample_column }}, locus)) %>%
    pivot_wider(names_from = locus, values_from = allele) %>%
    rename_with(~ str_replace(., "HLA\\-", "HLA_"))
}