R/IncorporateDepmap.R

In MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

#' Incorporate Depmap screen into analysis
#'
#' @docType methods
#' @name IncorporateDepmap
#' @rdname IncorporateDepmap
#'
#' @param dd A data frame.
#' @param symbol A character, specifying the column name of gene symbols in the data frame.
#' @param cell_lines A character vector, specifying the cell lines in Depmap to be considered.
#' @param lineages A character vector, specifying the lineages in Depmap to be considered.
#' @param na.rm Boolean, indicating whether removing NAs from the results.
#' @author Wubing Zhang
#'
#' @return A data frame with Depmap column attached.
#'
#' @examples
#' file1 = file.path(system.file("extdata", package = "MAGeCKFlute"),
#' "testdata/rra.gene_summary.txt")
#' gdata = ReadRRA(file1)
#' head(gdata)
#' \dontrun{
#'   gdata = IncorporateDepmap(gdata)
#'   head(gdata)
#' }
#' @export
#'
IncorporateDepmap <- function(dd, symbol = "id",
                              cell_lines = NA, lineages = "All",
                              na.rm = FALSE){
  ## Load Depmap data
  depmap_rds = file.path(system.file("extdata", package = "MAGeCKFlute"), "Depmap_19Q3.rds")
  if(file.exists(depmap_rds)){
    Depmap_19Q3 = readRDS(depmap_rds)
  }else{
    Depmap_19Q3 = t(read.csv("https://ndownloader.figshare.com/files/20234073", header = TRUE,
                             row.names = 1, stringsAsFactors = FALSE, check.names = FALSE))
    rownames(Depmap_19Q3) = gsub(" .*", "", rownames(Depmap_19Q3))
    saveRDS(Depmap_19Q3, depmap_rds)
  }
  meta_rds = file.path(system.file("extdata", package = "MAGeCKFlute"), "Depmap_sample_info.rds")
  if(file.exists(meta_rds)){
    sampleinfo = readRDS(meta_rds)
  }else{
    sampleinfo = read.csv("https://ndownloader.figshare.com/files/20274744",
                          row.names = 1, header = TRUE, stringsAsFactors = FALSE)
    saveRDS(sampleinfo, meta_rds)
  }
  sampleinfo = sampleinfo[colnames(Depmap_19Q3), ]
  idx1 = sampleinfo$lineage%in%lineages
  idx2 = sampleinfo$stripped_cell_line_name%in%cell_lines |
    sampleinfo$CCLE.Name%in%cell_lines |
    sampleinfo$alias%in%cell_lines
  genes = as.character(dd[, symbol])
  Depmap_19Q3 = as.data.frame(Depmap_19Q3, stringsAsFactors = FALSE)
  if(sum(idx2)>0){
    dd = cbind(dd, Depmap = rowMeans(Depmap_19Q3[genes, idx2], na.rm = TRUE))
  }else if(sum(idx1)>0){
    dd = cbind(dd, Depmap = rowMeans(Depmap_19Q3[genes, idx1], na.rm = TRUE))
  }else{
    dd = cbind(dd, Depmap = rowMeans(Depmap_19Q3[genes, ], na.rm = TRUE))
  }
  if(na.rm) dd = na.omit(dd)
  return(dd)
}