R/Parser4frma.R

#Use frma method to do normalization
#' Title
#'
#' @return
#' @export
#'
#' @examples
#' Parser4frma("/media/H_driver/2015/Sophia/Cel_file_frma/",cel.file.name.key.set.symbol.st134,
#' "heatmap_allsample_frma_2.pdf","PCA_allsample_frma_2.pdf","/media/H_driver/2015/Sophia/Results/")
#'
Parser4frma <- function(dir_cel_file_frma,cel.file.name.key.set.symbol.st134,heatmap_output_file,PCA_output_file,output_dir_re) {
  setwd(dir_cel_file_frma)
  data.set123.raw <- ReadAffy()
  data.set123.frma<-frma(data.set123.raw)
  ed.set123.frma <- exprs(data.set123.frma)
  samp.frma <- sampleNames(data.set123.frma)
  probes.frma <- featureNames(data.set123.frma)

  samp.frma.1<-gsub(" - ","_",samp.frma)
  samp.frma.2<-gsub(".CEL","",samp.frma.1)
  samp.frma.3<-gsub(".cel","",samp.frma.2)
  samp.frma.4<-gsub("-","_",samp.frma.3)
  samp.frma.5<-cbind(samp.frma,samp.frma.4)

  samp.frma.cancer.index<-which(samp.frma.5[,2] %in% cel.file.name.key.set.symbol.st134[,1])

  samp.frma.6<-samp.frma.5[samp.frma.cancer.index,]

  data.set123.frma.cancer<-data.set123.frma[,samp.frma.cancer.index]
  ed.set123.frma.cancer<-ed.set123.frma[,samp.frma.cancer.index]

  samp.frma.7<-cbind(samp.frma.6,colnames(ed.set123.frma.cancer))
  samp.frma.8<-samp.frma.7[,2:3]
  colnames(samp.frma.8)<-c("key","filename_frma")

  cel.file.sample.infor.no.8<-merge(cel.file.name.key.set.symbol.st134,samp.frma.8,by="key",sort=FALSE)

  GeneSym.all <- getSYMBOL(rownames(ed.set123.frma.cancer), "hgu133plus2.db")
  ndata<-ed.set123.frma.cancer
  geneSymbol=GeneSym.all
  tempdata.byGSym = data.frame(ndata, Symbol = geneSymbol)
  tempdata.byGSym.2<-tempdata.byGSym[-which(is.na(tempdata.byGSym$Symbol)),]
  rownames(tempdata.byGSym.2) = NULL
  data.byGSym = ddply(tempdata.byGSym.2, c("Symbol"),function(h)
    summary = apply(h,2,max)
  )

  rownames(data.byGSym)=data.byGSym$Symbol
  data.byGSym.2<-data.byGSym[,-dim(data.byGSym)[2]]
  temp = apply(data.byGSym.2,2,as.numeric)
  rownames(temp) = rownames(data.byGSym.2)
  data.byGSym.2 = temp
  SampleType<-cel.file.sample.infor.no.8$subtype
  heatmap_wPCA(data.byGSym.2,heatmap_output_file,PCA_output_file,output_dir_re,SampleType)

}
aiminy/Sophia documentation built on May 10, 2019, 7:39 a.m.