R/scores.R

In elimereu/matchSCore2: What the Package Does TODOELI

#' Compute matchSCore for different thresholds of specificity and ntop ranked genes
#'
#' This function computes the matchSCore for different cutoffs of marker specificity
#' and top cluster markers
#' @param sim A Splatter simulation object.
#' @param tool_out The output of the used tool to cluster your data (It should be
#' as the output of the `seurat3_run` function).
#' @param ntop A vector with different proportions of top-ranked markers for each
#' cluster. Usually `seq(250,2000,250)`.
#' @param tool_run The name of the function used to run the clusters without
#' quote (Defaults to `seurat3_run`).
#' @param labels Cluster labels as in the output of the [compute_labels()] function.
#'
#' @return A matrix. Each row contains the matchSCore at the specified level of
#' specificity and `ntop`.
#'
#' @export
#'
#' @examples
#' # TODO
scores <- function(sim,
                   tool_out,
                   ntop,
                   tool_run = seurat3_run,
                   labels) {
  for (y in seq(0.1, 1, 0.1)) {
    score <- sapply(ntop, function(x) tool_scores_by_specificity(sim, specificity = y, tool_out, x, seurat3_run, labels))
    if (y == 0.1) {
      s <- cbind(specificity = rep(y, length(ntop)), ntop, score)
    } else {
      s <- rbind(s, cbind(specificity = rep(y, length(ntop)), ntop, score))
    }
  }

  return(s)
}