R/utils.R

In barupal/MetSkye:

## few helpful functions for processing of raw LC/GC ms data files.

#' Extract time stamps from Agilent LCMC data files (.D). For QC based normalization in metabolomics, it is required to have exact time at which raw data were acquired so QC and study samples can be ordered accordingly. This simple function extracts the timestamps from .D file for Agilent LCMS files.
#'
#' @param dataDir - path to the data folder where .D files are located.
#' @return file and time-stamp values in timeStamps.txt
#' @examples
#' extractTimeStampsAgilent("/path/to/agilent/data/files")

extractTimeStampsAgilent <- function(datadir) {
  filelist <- dir(dataDir)
  library(XML)
  con1 <- file(paste0(dataDir,"timeStamps.txt"),"w")
  for (i in 1:length(filelist)) {
    xfile <- xmlToList(paste0(dataDir,filelist[i]))
    writeLines(paste(xfile[3]$Field$Value,xfile[24]$Field$Value, sep="\t"), con1)
    print(i)
  }
  close(con1)
}