Comparative_MEA_dataset/Codes/meaRtools/cheminfo.R

cheminfo<-function (file, masterChemFile = masterChemFile) 
  #function from IGM.MEA package 
{
  masterChem = read.csv(masterChemFile)
  masterCD <- as.data.frame(masterChem)
  masterCD <- masterCD[, 1:9]
  temp1 <- paste(masterCD$Project, masterCD$Experiment.Date, 
                 masterCD$Plate.SN, sep = "_")
  masterCD$filenames <- temp1
  masterCD <- masterCD[order(masterCD$Experiment.Date, masterCD$Plate.SN, 
                             masterCD$Well), ]
  shortFileName <- paste(strsplit(basename(file), "_")[[1]][1], 
                         strsplit(basename(file), "_")[[1]][2], strsplit(basename(file), 
                                                                         "_")[[1]][3], sep = "_")
  plate.chem.info <- list()
  count = 1
  matchedFileName = 0
  for (i in which(shortFileName == masterCD$filename)) {
    matchedFileName = 1
    plate.chem.info$well[count] <- paste(masterCD$Well[i])
    plate.chem.info$treatment[count] <- paste(masterCD$Treatment[i])
    plate.chem.info$size[count] <- paste(masterCD$Size[i])
    plate.chem.info$dose[count] <- paste(masterCD$Dose[i])
    plate.chem.info$units[count] <- paste(masterCD$Units[i])
    count = count + 1
  }
  if (matchedFileName == 0) {
    print(paste("File ", shortFileName, " was not found in the possible file names \n                  constructed from exp log file:", 
                unique(masterCD$filename), sep = ""))
  }
  if (!is.element(length(plate.chem.info$well), c(12, 48))) {
    print(paste("Info exists for ", length(plate.chem.info$well), 
                " wells; Some wells have no data.", sep = ""))
  }
  plate.chem.info
}