R/rank_sim.R

In elimereu/matchSCore2: What the Package Does TODOELI

#' Rank simulated group markers
#'
#' This function rank group markers according their relative specificity based
#' on fold changes.
#'
#' @param sim A Splatter sim object with simulated cellular groups or paths.
#'
#' @return A `data.frame` containing the group gene ranking and other additional
#' information for each gene from the simulated data set.
#'
#' @export
#'
#' @examples
#' # TODO
rank_sim <- function(sim) {
  pd <- colData(sim)
  fd <- rowData(sim)
  group <- factor(pd$Group)
  l <- length(levels(group))
  ng <- length(fd$Gene)

  fc <- fd[, grep("^DEFac", names(fd))]

  de <- sapply(1:l, function(x) ifelse(fc[, x] > 1, 1, 0))
  rank_info <- sapply(1:l, function(x) ifelse(de[, x] * rowSums(de) >= 1, rowSums(de), l * 10))
  rank_info <- data.frame(fc, rank_info)

  ord <- sapply(1:l, function(x) order(rank_info[, (x + l)], -rank_info[, x]))
  rank <- apply(ord, 2, function(x) order(x))

  rank_df <- data.frame(fd[, c(1:4)], r_info = rank_info, rank_info, Rank = rank)

  return(rank_df)
}