R/ReadsgRRA.R

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

#' Read sgRNA summary in MAGeCK-RRA results
#'
#' @docType methods
#' @name ReadsgRRA
#' @rdname ReadsgRRA
#'
#' @param sgRNA_summary A file path or a data frame of sgRNA summary data.
#'
#' @return A data frame.
#'
#' @author Wubing Zhang
#'
#' @examples
#' file2 = file.path(system.file("extdata", package = "MAGeCKFlute"),
#'                   "testdata/rra.sgrna_summary.txt")
#' sgrra = ReadsgRRA(file2)
#' head(sgrra)
#'
#' @export
#'
ReadsgRRA <- function(sgRNA_summary){
  if(is.null(dim(sgRNA_summary))){
    sgRNA_summary = read.table(file = sgRNA_summary, sep = "\t", header = TRUE, quote = "",
                    comment.char = "", check.names = FALSE, stringsAsFactors = FALSE)
  }
  dd = sgRNA_summary[, c("sgrna", "Gene", "LFC", "FDR")]
  return(dd)
}