L1kProcs/Preprocess.R at master · Su-informatics-lab/L1kProcs · GitHub

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Preprocess <- function(iStart,iEnd,Path,Overwrite){
# Processing all KD data
setwd(Path)
suppressMessages(library(preprocessCore))
suppressMessages(library(stats))
suppressMessages(library(prada))
source("Util.R")
# Files & Directories:
#   ../Annotation/bead_gene_map.csv
#   ../Annotation/HG_U133A.chip
#   ../Annotation/plate_maps.csv
#   ../Annotation/plate_list.csv
#   ../Output/dataName.csv
#   ../Output/dataName.gct

## ifBead2Gene <- "../Annotation/bead_gene_map.csv"
## ifU133A <- "../Annotation/HG_U133A.chip"
## ifPlateMap <- "../Annotation/plate_maps.csv"
## ifPlateList <- "../Annotation/plate_list.csv"
## Bead2Gene <- read.csv(ifBead2Gene, header = TRUE, stringsAsFactors = FALSE)
## PlateMap <- read.csv(ifPlateMap, header = TRUE, stringsAsFactors = FALSE)
## U133A <- read.delim(ifU133A, header = TRUE, stringsAsFactors = FALSE)
## rownames(U133A) <- U133A$pr_id


if (!file.exists("lstNames.RData")){
  cat("Please save all the data to lstNames.Data first!\n")
}

load(file = "lstNames.RData")


for (DataName in lstNames[iStart:iEnd]){
  LXB2Stats(DataName,Overwrite)
}

for (DataName in lstNames[iStart:iEnd]){
  Stats2gct(DataName,Overwrite)
}
}