R/read_sumstats.R

In pleioh2g: Estimation of Pleiotropic Heritability from Genome-Wide Association Studies (GWAS) Summary Statistics

#' Read summary statistics from either internal or external file - refer to ldscr R package (https://github.com/mglev1n/ldscr)
#' @description
#' `read_sumstats()` Read summary statistics from either internal or external file

#' @param munged_sumstats Either a dataframe, or a path to a file containing munged summary statistics. Must contain at least columns named `SNP` (rsid), `A1` (effect allele), `A2` (non-effect allele), `N` (total sample size) and `Z` (Z-score)
#' @param name trait name
#' @return
#' A data frame (tibble) containing GWAS summary statistics for the specified trait.
#' The returned object will always contain at least the following columns:
#' \itemize{
#'   \item \code{SNP}: SNP identifier (rsID).
#'   \item \code{A1}: Effect allele.
#'   \item \code{A2}: Non-effect allele.
#'   \item \code{N}: Total sample size for the SNP.
#'   \item \code{Z}: Z-score of SNP-trait association.
#' }
#' @export

read_sumstats <- function(munged_sumstats, name) {
  # Check if name is present to enable more informative logging
  if (missing(name)) {
    if (is.character(munged_sumstats)) {
      cli::cli_progress_step("Reading summary statistics from {munged_sumstats}")
      sumstats_df <- vroom::vroom(munged_sumstats, col_types = vroom::cols())
    } else {
      cli::cli_progress_step("Reading summary statistics from dataframe")
      sumstats_df <- munged_sumstats
    }
  } else {
    if (is.character(munged_sumstats)) {
      cli::cli_progress_step("Reading summary statistics for '{name}' from {munged_sumstats}")
      sumstats_df <- vroom::vroom(.x, col_types = vroom::cols())
    } else {
      cli::cli_progress_step("Reading summary statistics for '{name}' from dataframe")
      sumstats_df <- .x
    }
    sumstats_df <- na.omit(sumstats_df)

    return(sumstats_df)
  }
}