R/parser.R

In lwaldron/ccleWrap: wrapper structures and functions for Broad/Novartis CCLE resources

csvname="CCLE_NP24.2009_Drug_data_2012.02.20.csv"
csvhash.md5="b64295ef99912d1d4bead76461d0e2a1"

parseCCLEline = function(dfline, validateNames=FALSE) {
  # parse a row of ccle CSV import
  if (nrow(dfline)!=1 || !is.data.frame(dfline)) 
    stop("input must be 1line data.frame")
  jan2013names = c("CCLE.Cell.Line.Name", "Primary.Cell.Line.Name", "Compound", 
                   "Target", "Doses..uM.", "Activity.Data..median.", "Activity.SD", 
                   "Num.Data", "FitType", "EC50..uM.", "IC50..uM.", "Amax", "ActArea"
  )
  if (validateNames && !isTRUE(all.equal(names(dfline), jan2013names)))
    warning("it appears the names of the input data.frame do not agree with expectation")
  getOrgan = function(x) {x = sub("_", "@@", x); gsub(".*@@", "", x) }
  cvec = as.character(dfline)
  cvec[cvec=="NA"] <- NA
  new("ccleExpt",
      organ=getOrgan(cvec[1]),
      line=cvec[2], compound=cvec[3],
      target = cvec[4], doses_uM=.nstring2vec(cvec[5]),
      activityMedian=.nstring2vec(cvec[6]),
      activitySD=.nstring2vec(cvec[7]),
      fitType=cvec[9],
      EC50_uM = as.numeric(cvec[10]),
      IC50_uM = as.numeric(cvec[11]),
      Amax = as.numeric(cvec[12]),
      ActArea = as.numeric(cvec[13]))
}