R/summarise_gcae_input_data.R

In richelbilderbeek/gcaer: Interface to GCAE

#' Summarise the `gcae_input_data`
#'
#' Summarise the `gcae_input_data`
#' @inheritParams default_params_doc
#' @return This function will show the summary using \link{message}.
#' A \link{list} with all the elements shown is returned as well
#' @note this function is named after the base R \link{summarise} function
#' @examples
#' gcae_input_data <- create_test_gcae_input_data()
#' summarise_gcae_input_data(gcae_input_data)
#' @author Richèl J.C. Bilderbeek
#' @export
summarise_gcae_input_data <- function(
  gcae_input_data,
  verbose = FALSE
) {
  # gcae_input_data can be invalid, which is _why_ we resize
  gcaer::check_gcae_input_data_data_type(gcae_input_data)

  if (sum(is.na(gcae_input_data$phe_table)) != 0) {
    stop(
      "'gcae_input_data$phe_table' must not contain NAs. \n",
      "Found ", sum(is.na(gcae_input_data$phe_table)), " NAs"
    )
  }
  gcae_input_data$phe_table
  summary <- list(
    n_individuals_in_bed_table = ncol(gcae_input_data$bed_table),
    n_snps_in_bed_table = nrow(gcae_input_data$bed_table),
    n_snps_in_bim_table = nrow(gcae_input_data$bim_table),
    n_individuals_in_fam_table = nrow(gcae_input_data$fam_table),
    n_individuals_in_phe_table = nrow(gcae_input_data$phe_table)
  )

  if ("labels_table" %in% names(gcae_input_data)) {
    summary$n_populations_in_labels_table <- nrow(gcae_input_data$labels_table)
    summary$n_superpopulations_in_labels_table <- length( # nolint indeed a long variable name
      unique(gcae_input_data$labels_table$super_population)
    )
  }

  if (verbose) {
    for (i in seq_along(summary)) {
      message(names(summary)[i], ": ", summary[[i]])
    }
  }
  summary
}