R/getMegaProfData.R

In bioCancer: Interactive Multi-Omics Cancers Data Visualization and Analysis

#' search and get genetic profiles (CNA,mRNA, Methylation, Mutation...) of gene list upper than 500
#'
#' @details See \url{https://github.com/kmezhoud/bioCancer/wiki}
#'
#' @return A data frame with Genetic profile
#'
#' @usage getMegaProfData(MegaGeneList, GenProf, Case, Class)
#' @param MegaGeneList A list of genes upper than 500
#' @param GenProf genetic profile reference
#' @param Case  Case reference
#' @param Class indicates the panel ProfData or Mutdata
#'
#' @examples
#' GeneList <- c("ALK", "JAK3", "SHC3","TP53","MYC","PARP")
#' \dontrun{
#' cgds <- cgdsr::CGDS("http://www.cbioportal.org/")
#' listCase_gbm_tcga_pub <- cgdsr::getCaseLists(cgds,"gbm_tcga_pub")[,1]
#' listGenProf_gbm_tcga_pub <- cgdsr::getGeneticProfiles(cgds,"gbm_tcga_pub")[,1]
#'
#' ProfData_Mut <- grepRef("gbm_tcga_pub_all", listCase_gbm_tcga_pub,
#'  "gbm_tcga_pub_mutations", listGenProf_gbm_tcga_pub, GeneList, Mut=1)
#'}
#'@export

getMegaProfData <- function(MegaGeneList,GenProf, Case, Class){


  if(is.integer(length(MegaGeneList)/500)){

    G <- length(MegaGeneList)/500
  }else{
    G <- as.integer(length(MegaGeneList)/500) + 1

  }
  # if(input=="Class"){
  #   GenProf <- input$GenProfsIDClassifier[s]
  #   Case <- input$CasesIDClassifier[s]
  # }else if(input=="ProfData"){
  #   GenProf <- input$GenProfID
  #   Case <- input$CasesID
  #
  # }

  MegaProfData <- 0
  SubMegaGeneList <- 0
  for(g in 1: G){

    if (length(MegaGeneList) - length(SubMegaGeneList) > 500){
      SubMegaGeneList <- MegaGeneList[(((g-1)*500)+1):((g)*500)]
    } else{
      SubMegaGeneList <- MegaGeneList[(((g-1)*500)+1):length(MegaGeneList) ]
    }


    print(paste("Getting Profile Data of Genes from: ", (((g-1)*500)+1), "to",((g)*500), sep= " "))

    if(Class=="ProfData"){
      ProfData<-cgdsr::getProfileData(cgds,SubMegaGeneList, GenProf,Case)
      MegaProfData <- cbind(MegaProfData, ProfData)

    }else if(Class=="MutData"){
      if (inherits(try(ProfData <- cgdsr:: getMutationData(cgds,Case, GenProf, SubMegaGeneList), silent=FALSE),"try-error")){
        msgbadGeneList <- "There are some Gene Symbols not supported by cbioportal server"
        #tkmessageBox(message=msgbadGeneList, icon="warning")

      }else{
        ProfData <- cgdsr::getMutationData(cgds,Case, GenProf, SubMegaGeneList)
      }
      MegaProfData <- rbind(MegaProfData, ProfData)
    }

  }

  if(Class=="ProfData"){
    MegaProfData <- MegaProfData[,-1]
  }else if (Class=="MutData"){
    MegaProfData <- MegaProfData[-1,]

  }
  MegaProfData <- round(MegaProfData, digits = 3)

  return(MegaProfData)


}