R/Proce_cli.R

In GeoTcgaData: Processing various types of data on GEO and TCGA

#' Combine clinical information obtained from TCGA and extract survival data
#'
#' @param Files_dir a dir data
#'
#' @return a matrix, survival time and survival state in TCGA
#' @export
#'
#' @examples
#' tcga_cli_deal(system.file(file.path("extdata","tcga_cli"),package="GeoTcgaData"))
tcga_cli_deal<-function(Files_dir = "your_clinical_directory"){
    if(Files_dir!="your_clinical_directory") {
        out <- file.path(tempdir(), "clin2.txt")
        Files <- dir(Files_dir)
        file_id <- Files
        #Modify an error
        for(i in 1:length(file_id)){
            file_id[i]<-unlist(strsplit(file_id[i],"\\."))[3]
        }
        time<-"</clin_shared:days_to_last_followup>"
        state<-"</clin_shared:vital_status>"
      
        days="</clin_shared:days_to_death>"
        for(file in Files){
            #haha means the sample has no survival data
            timee <- "haha"
            statee <- "haha"
            aa<-as.matrix(utils::read.table(file.path(Files_dir,file),sep="\t",header=T))
            for(i in 1:dim(aa)[1]){
                if(length(grep(time,aa[i,1]))>0){
                     timee<-unlist(strsplit(aa[i,1],">"))[2]
        
                     timee<-gsub("</clin_shared:days_to_last_followup","",timee)
                }
            }
        
            for(i in 1:dim(aa)[1]){
                if(length(grep(state,aa[i,1]))>0){
                     statee<-unlist(strsplit(aa[i,1],">"))[2]
        
                     statee<-gsub("</clin_shared:vital_status","",statee)
                }
            }
                for(i in 1:dim(aa)[1]){
                if(length(grep(days,aa[i,1]))>0){
                     timee<-unlist(strsplit(aa[i,1],">"))[2]
        
                     timee<-gsub("</clin_shared:days_to_death","",timee)
                }
            }
            file_idd<-unlist(strsplit(file,"\\."))[3]
        
            utils::write.table(cbind(file_idd,timee,statee),out,
	              sep="\t",row.names=FALSE,col.names=FALSE,append=TRUE,quote=FALSE)
        }
        output_cli <- data.table::fread(out,sep="\t",header=F)
        file.remove(out)
        return(output_cli)
} else {message("please give your directory!")} }