R/getTransGenePredictorFile.R

In bozdaglab/miRDriver: miRDriver: A Tool to Infer Copy Number Derived miRNA-Gene Networks in Cancer

## miRDriver STEP 4
## Code 1
## Created By: Banabithi Bose
## Date Created: 5/1/2019
getTransGenePredictorFile <-
  function(ncore = 2,
           methylationData,
           RSeqData,
           CNVData,
           TFData,minConfidenceTF = 5,
           mirnaData,
           mirdirectory = "~") {
    if (is(methylationData, "SummarizedExperiment")) {
      methylationData <- assay(methylationData)
    } else {
      methylationData <- methylationData
    }
    
    if (is(RSeqData, "SummarizedExperiment")) {
      RSeqData <- assay(RSeqData)
    } else {
      RSeqData <- RSeqData
    }
    
    if (is(CNVData, "SummarizedExperiment")) {
      CNVData <- assay(CNVData)
    } else {
      CNVData <- CNVData
    }
    
    if (is(TFData, "SummarizedExperiment")) {
      TFData <- assay(TFData)
    } else {
      TFData <- TFData
    }
    # Filtering TFData based on confidence score
    
     TFData <- TFData[TFData$Confidence >= minConfidenceTF,][,-3,drop=FALSE] 
    
    
    if (is(mirnaData, "SummarizedExperiment")) {
      mirnaData <- assay(mirnaData)
    } else {
      mirnaData <- mirnaData
    }
    
    ..tf <- processEachGene <- NULL
    
    if (!file.exists(file.path(
      mirdirectory,
      "mirDriverFold",
      "miRDriver_Step4",
      fsep = .Platform$file.sep
    ))) {
      dir.create(
        file.path(
          mirdirectory,
          "mirDriverFold",
          "miRDriver_Step4",
          fsep = .Platform$file.sep
        )
      )
    }
   
    if (!file.exists(file.path(
      mirdirectory,
      "mirDriverFold",
      "miRDriver_Step4",
      "TransGenePredFile",
      fsep = .Platform$file.sep
    ))) {
      dir.create(
        file.path(
          mirdirectory,
          "mirDriverFold",
          "miRDriver_Step4",
          "TransGenePredFile",
          fsep = .Platform$file.sep
        )
      )
    } 
    
    
    processEachGene <- function(GeneFile) {
      tryCatch({
        methylation <- methylationData
        RSeq <- RSeqData
        CNV <- CNVData
        TF <- TFData
        MG <- mirnaData
        load(
          file.path(
            mirdirectory,
            "mirDriverFold",
            "miRDriver_Step3",
            "gene_all_mirna",
            GeneFile
          )
        )
        colnames(GM) <- "miRNA_ID"
        mirna <- data.frame(colnames(MG[,-1]))
        colnames(mirna) <- "miRNA"
        mirna$miRNA <- as.character(mirna$miRNA)
        common <- intersect(GM$miRNA_ID, mirna$miRNA)
        GeneMirnaData <- MG[, ..common]
        
        if (nrow(GeneMirnaData) != 0) {
          GeneMirnaData <- cbind(MG[, 1, drop = FALSE], MG[, ..common])
          MG <- data.table(MG)
          GeneMirnaData1 <- MG[, ..common]
          load(
            file.path(
              mirdirectory,
              "mirDriverFold",
              "miRDriver_Step3",
              "gene_all_DEcis",
              GeneFile
            )
          )
          colnames(TC) <- "cis_gene"
          all_genes <- data.frame(colnames(RSeq[,-1]))
          colnames(all_genes) <- "gene"
          common <- intersect(TC$cis_gene, all_genes$gene)
          CisGene <- RSeq[, common]
          if (ncol(CisGene) == 0) {
            CisGeneData <- RSeq[, 1, drop = FALSE]
          } else {
            CisGeneData <- cbind(RSeq[, 1, drop = FALSE], RSeq[, common])
          }
          Geneid <- str_sub(GeneFile, end = -5)
          if (is.element(Geneid, colnames(methylation))) {
            MethGene <- methylation[, ..Geneid]
            MethGene <- na.omit(MethGene)
            if (nrow(MethGene) == 0) {
              MethGeneData <- methylation[, 1, drop = FALSE]
            } else{
              MethGeneData <-
                cbind(methylation[, 1, drop = FALSE], methylation[, ..Geneid])
              colnames(MethGeneData) <- c("sample", "beta")
            }
          } else{
            MethGeneData <- methylation[, 1, drop = FALSE]
          }
          if (is.element(Geneid, colnames(CNV))) {
            cnvGene <- CNV[, ..Geneid]
            cnvGene <- na.omit(cnvGene)
            if (nrow(cnvGene) == 0) {
              CNVGeneData <- CNV[, 1, drop = FALSE]
            } else{
              CNVGeneData <- cbind(CNV[, 1, drop = FALSE], CNV[, ..Geneid])
              colnames(CNVGeneData) <- c("sample", "cnv")
            }
          } else{
            CNVGeneData <- CNV[, 1, drop = FALSE]
          }
          TF <- data.frame(TF)
          tfGene <- TF[TF$gene_id == Geneid,]
          if (nrow(tfGene) == 0) {
            tfGeneData <- RSeq[, 1, drop = FALSE]
          } else{
            tf <- tfGene$TF
            if (is.element(tf, colnames(RSeq))) {
              tfGeneData <- cbind(RSeq[, 1, drop = FALSE], RSeq[, ..tf])
            } else{
              tfGeneData <- RSeq[, 1, drop = FALSE]
            }
          }
          if (is.element(Geneid, colnames(RSeq))) {
            Y <- cbind(RSeq[, 1, drop = FALSE], RSeq[, Geneid])
          }
          V1 <- GeneMirnaData
          V2 <- CisGeneData
          V3 <- MethGeneData
          V4 <- CNVGeneData
          V5 <- tfGeneData
          Y$sample <- as.character(Y$sample)
          V1$sample <- as.character(V1$sample)
          V2$sample <- as.character(V2$sample)
          V3$sample <- as.character(V3$sample)
          V4$sample <- as.character(V4$sample)
          V5$sample <- as.character(V5$sample)
          Y <- data.frame(unique(Y))
          colnames(Y) <- c("sample", Geneid)
          V1 <- data.frame(unique(V1))
          V2 <- data.frame(unique(V2))
          V3 <- data.frame(unique(V3))
          V4 <- data.frame(unique(V4))
          V5 <- data.frame(unique(V5))
          dfs <- list(Y, V1, V2, V3, V4, V5)
          df <-
            Reduce(function(...)
              merge(..., by = "sample", x.all = TRUE), dfs)
          df <- remove_empty(df, c("rows", "cols"))
          GenePred <- df[complete.cases(df), ]
          save(
            GenePred,
            file = file.path(
              mirdirectory,
              "mirDriverFold",
              "miRDriver_Step4",
              "TransGenePredFile",
              paste0(Geneid, ".Rda")
            )
          )
        }
      }, error = function(error_condition) {
        cat(
          paste0(GeneFile, " : ", error_condition),
          file = file.path(
            mirdirectory,
            "mirDriverFold",
            "ERROR_FILES",
            "Step4_transGenePredictorError.txt",
            fsep = .Platform$file.sep
          ),
          sep = "\n",
          append = TRUE
        )
      }, finally = {
        
      })
    }
    if (ncore > 1) {
      cl <-
        makeCluster(mc <- getOption("cl.cores", ncore))
      
      invisible(clusterEvalQ(cl, library(glmnet)))
      invisible(clusterEvalQ(cl, library(janitor)))
      invisible(clusterEvalQ(cl, library(stringr)))
      invisible(clusterEvalQ(cl, library(data.table)))
      invisible(clusterEvalQ(cl, library(gsubfn)))
      invisible(clusterEvalQ(cl, library(parallel)))
      invisible(clusterEvalQ(cl, library(sqldf)))
      invisible(clusterEvalQ(cl, library(reshape)))
      invisible(clusterEvalQ(cl, library(reshape2)))
      parallel::clusterExport(
        cl = cl,
        c(
          "methylationData",
          "RSeqData",
          "CNVData",
          "TFData",
          "mirnaData"
        ),
        envir = environment()
      )
      GeneFileNames <-
        list.files(
          file.path(
            mirdirectory,
            "mirDriverFold",
            "miRDriver_Step3",
            "gene_all_mirna"
          ),
          pattern = "*.Rda"
        )
      parLapply(cl, GeneFileNames, processEachGene)
      stopCluster(cl)
    }
    else {
      GeneFileNames <-
        list.files(
          file.path(
            mirdirectory,
            "mirDriverFold",
            "miRDriver_Step3",
            "gene_all_mirna"
          ),
          pattern = "*.Rda"
        )
      lapply(GeneFileNames, processEachGene)
    }
    return(
      paste0(
        "All predictors are gathered for trans genes in mirDriverFold/miRDriver_Step4/TransGenePredFile"
      )
    )
  }