R/batch_quantnorm.R

In batchtma: Batch Effect Adjustments

#' Helper function for approach 6: Quantile normalize
#'
#' @param var Single variable to quantile-normalize
#' @param batch Variable indicating batch
#'
#' @return Tibble of means per batch for one variable
#' @noRd
batch_quantnorm <- function(var, batch) {
  df <- tibble::tibble(var, batch) |>
    tibble::rowid_to_column() |>
    tidyr::pivot_wider(
      names_from = batch,
      values_from = var
    ) |>
    dplyr::select(!"rowid") |>
    dplyr::select(dplyr::where(\(x) !all(is.na(x)))) |>
    as.matrix() |>
    limma::normalizeQuantiles() |>
    tibble::as_tibble()

  df |>
    dplyr::mutate(
      result = purrr::pmap_dbl(
        .l = df,
        .f = function(...) {
          mean(c(...), na.rm = TRUE)
        }
      ),
      result = dplyr::if_else(
        is.nan(.data$result),
        true = NA_real_,
        false = .data$result
      ),
      .keep = "none"
    ) |>
    dplyr::pull(.data$result)
}