R/return_markers.R

In kgellatl/SignallingSingleCell: Network Analysis for single cell RNA sequencing Data (sc-RNASeq)

#' Return markers
#'
#' This will return the marker genes.
#'
#' @param input the input ex_sc
#' @param return_by the pData column that was used for id_markers (id_by argument)
#' @param num_markers the number of markers to return for each cell type
#' @export
#' @details
#' This will return the marker and reference genes stored in fData(input) in a convienient list format.
#' @examples
#' marker_list <- return_markers(input = ex_sc, num_markers = 50)

return_markers <- function(input, return_by = "Cluster", num_markers = 10){
  dat <- fData(input)
  Clusters <- (unique(pData(input)[,return_by]))
  Clusters <- as.character(Clusters)
  Clusters <- sort(Clusters)
  markers <- vector(mode = "list", length = length(Clusters))
  for(i in 1:length(Clusters)){
    cint <- Clusters[i]
    ind <- grep(paste0("^", cint, "_marker_score_", return_by, "$"), colnames(dat))
    ind2 <- match(seq(1:num_markers), dat[,ind])
    marker_final <- rownames(dat)[ind2]
    markers[[i]] <- marker_final
  }
  names(markers) <- c(paste0(Clusters, "_Markers"))
  return(markers)
}