R/getGenProfs.R

In canceR: A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC

#' Get Genetic Profile from selected Studies
#' @usage getGenProfs()
#' @return dataframe with genetic profil
#' @export
#' @examples
#' cgds<-CGDS("http://www.cbioportal.org/")
#' # Get list of cancer studies at server
#' Studies <- getCancerStudies(cgds)[,2]
#' # Get available case lists (collection of samples) for a given cancer study
#' mycancerstudy <- getCancerStudies(cgds)[2,1]
#' mycaselist <- getCaseLists(cgds,mycancerstudy)[1,1]
#' # Get available genetic profiles
#' mygeneticprofile <- getGeneticProfiles(cgds,mycancerstudy)[4,1]
#' \dontrun{
#' getGenProfs()
#' }
getGenProfs <- function(){
    
    #get Study Index
    StudiesRef <- cgdsr::getCancerStudies(myGlobalEnv$cgds)[,1]

    ## and we need the cases list of every study
    myGlobalEnv$checked_Studies_forGenProf <- myGlobalEnv$checked_Studies
    myGlobalEnv$lchecked_Studies_forGenProf <- length(myGlobalEnv$checked_Studies_forGenProf)

   police <- tkfont.create(family="arial", size=11)
   tkconfigure(myGlobalEnv$tl, foreground="black", font=police)


    GenProfsStudies = 0
    GenProfsRefStudies = 0
    LGenProfs= 0
    for (i in 1:(myGlobalEnv$lchecked_Studies_forGenProf)){

        Si = myGlobalEnv$checked_StudyIndex[i]

        tkinsert(myGlobalEnv$tl,"end",paste("***** Study ", Si ," : ", myGlobalEnv$Studies[Si],"******"))

        LGenProfs[i]<- length(getGeneticProfiles.CGDS(myGlobalEnv$cgds, StudiesRef[Si])[,1])

        myGlobalEnv$LGenProfs[i] <- LGenProfs[i]
        print(paste("There are",myGlobalEnv$LGenProfs[i],"Genetics Profiles in", myGlobalEnv$Studies[Si],sep=" "))

        # create progress bar
        progressBar_GenProfs <- tkProgressBar(title = myGlobalEnv$Studies[Si], min = 0,
                                              max = LGenProfs[i], width = 400)


        GenProfRefStudy =0
        GenProfsStudy = 0
        GenProfsRefStudy =0
        j=0
        for (j in 1:LGenProfs[i]){

            Sys.sleep(0.1)
            setTkProgressBar(progressBar_GenProfs, j,
                             label=paste( round(j/LGenProfs[i]*100, 0),"% of Genetic Profiles"))



            GenProfStudy <- getGeneticProfiles.CGDS(myGlobalEnv$cgds, myGlobalEnv$checked_Studies_forGenProf[i])[,2][j]
            GenProfRefStudy <- getGeneticProfiles.CGDS(myGlobalEnv$cgds, myGlobalEnv$checked_Studies_forGenProf[i])[,1][j]

            tkinsert(myGlobalEnv$tl,"end",paste(j,":",GenProfStudy))
            GenProfsStudy <- cbind(GenProfsStudy, GenProfStudy)
            GenProfsRefStudy <- cbind(GenProfsRefStudy, GenProfRefStudy)
        }
        close(progressBar_GenProfs)

        GenProfsStudies <- cbind(GenProfsStudies, GenProfsStudy)
        GenProfsRefStudies <- cbind(GenProfsRefStudies, GenProfsRefStudy)
    }


    GenProfsRefStudies <- GenProfsRefStudies[-1]
    myGlobalEnv$GenProfsRefStudies <- GenProfsRefStudies
    myGlobalEnv$GenProfsStudies <-GenProfsStudies


}