R/tabSearch.R

In zji90/GSCA: GSCA: Gene Set Context Analysis

tabSearch <- function(keyword,chipdata,option="OR"){
      if(chipdata == "hgu133a") {
            if (!require(Affyhgu133aExpr)) {
                  stop("Affyhgu133aExpr Package is not found")
            } else {
                  data(Affyhgu133aExprtab)
                  tab <- Affyhgu133aExprtab
            }
      } else if(chipdata == "moe4302"){
            if (!require(Affymoe4302Expr)) {
                  stop("Affymoe4302Expr Package is not found")
            } else {
                  data(Affymoe4302Exprtab)
                  tab <- Affymoe4302Exprtab
            }
      } else if(chipdata == "hgu133A2"){
            if (!require(Affyhgu133A2Expr)) {
                  stop("Affyhgu133A2Expr Package is not found")
            } else {
                  data(Affyhgu133A2Exprtab)
                  tab <- Affyhgu133A2Exprtab
            }
      } else if(chipdata == "hgu133Plus2"){
            if (!require(Affyhgu133Plus2Expr)) {
                  stop("Affyhgu133Plus2Expr Package is not found")
            } else {
                  data(Affyhgu133Plus2Exprtab)
                  tab <- Affyhgu133Plus2Exprtab
            }
      } else {
            stop("Please enter valid name for chipdata. Current Supported chipdata: 'hgu133a', 'moe4302', 'hgu133Plus2', 'hgu133A2'")
      }
      
      if(is.null(keyword)) stop("Please enter keyword.")
      keyword <- as.character(keyword)
      keyword <- unique(c(keyword,unlist(strsplit(keyword,";"))))
      
      if(option=="OR"){
            tmp <- NULL
            for(i in 1:length(keyword)){
                  tmp <- rbind(tmp,tab[unique(c(grep(keyword[i],tab$SampleType,ignore.case=T),
                                                grep(keyword[i],tab$ExperimentID,ignore.case=T))),])
            }
      } else if(option=="AND"){
            tmp <- NULL
            for(i in 1:length(keyword)){
                  tmp <- c(tmp,unique(c(grep(keyword[i],tab$SampleType,ignore.case=T),
                                        grep(keyword[i],tab$ExperimentID,ignore.case=T))))
                  
            }
            tmp <- table(tmp)
            tmp <- tab[as.numeric(names(tmp)[tmp == length(keyword)]),]
      } else {
            stop("Please enter 'OR' or 'AND' for option.")
      }
      
      if(nrow(tmp)==0) stop("No matching samples found for keyword.")
      tmpdex <- unique(tmp$SampleType)
      
      output1 <- rep("0",length(tmpdex))
      output2 <- output1
      output3 <- rep(0,length(tmpdex))
      for(i in 1:length(tmpdex)){
            output2[i] <- tmpdex[i]
            output1[i] <- paste(unique(tmp[which(tmp$SampleType==tmpdex[i]),2]),
                                collapse=";")
            output3[i] <- sum(tab$SampleType==tmpdex[i])
      }
      output <- data.frame(output1,output2,output3,
                           stringsAsFactors=FALSE)
      colnames(output) <- c("ExperimentID","SampleType","SampleCount")
      return(output)
}