R/markers_by_specificity.R

In elimereu/matchSCore2: What the Package Does TODOELI

#' Simulated group markers
#'
#' This function gives you the ranked list of group markers at the specified
#' proportion of top markers (specificity)
#'
#' @param rank_df The data frame with the ranked group genes as returned by the
#' [rank_sim()] function.
#' @param spec The proportion of top ranked genes. It has to be a number between
#' 0 and 1.
#' @param n_clust The number of simulated cell groups.
#'
#' @return A list with `n_clust` elements representing their corresponding group
#' markers. Each element of the list contains the relative set of marker indexes
#' as ordered in the original `rowData(sim)`.
#' The list doesn't keep the order of the ranking.
#'
#' @export
#'
#' @examples
#' # TODO
markers_by_specificity <- function(rank_df,
                                   spec,
                                   n_clust) {
  k <- 5 + n_clust
  info <- rank_df[, c(k:(k + n_clust - 1))] ## order
  p <- grep("^Rank", names(rank_df))
  R <- rank_df[, p] ## rank

  sorted <- sapply(1:n_clust, function(x) order(R[, x]))
  k <- 10 * n_clust
  length <- sapply(1:n_clust, function(x) length(which(info[, x] < k)))

  l <- sapply(1:n_clust, function(x) round(spec * length[x]))
  markers <- lapply(1:n_clust, function(x) sorted[1:l[x], x])

  return(markers)
}