R/DataProcess.R

In MSstatsQC: Longitudinal system suitability monitoring and quality control for proteomic experiments

#' A data processing function
#'
#' @param data Comma-separated (*.csv), QC file format. It should contain a Precursor column and the metrics columns.
#' @return A data frame that processes using \code{input.sanity.check} function.
#' @export
#' @import dplyr
#' @examples
#' # The data is "S9Site54" which is defined in the package.
#' data <- DataProcess(S9Site54)

DataProcess <- function(data = NULL){
  if(is.null(data))
    return()
  ## save process output in each step #### creating a log file ########### from Meena's code
  allfiles <- list.files()

  num <- 0
  filenaming <- "./log/msstatsqc"
  finalfile <- "msstatsqc.log"

  while(is.element(finalfile,allfiles)) {
    num <- num+1
    finalfile <- paste(paste(filenaming,num,sep="-"),".log",sep="")
  }

  data <- input.sanity.check(data, finalfile)

  missing<-rowSums(is.na(data))
  data<-cbind(data,missing)
  return(data)
}