def NCRNAAnnot (
      expression: CSV ,
      gtf: BinaryFile ,
      knownFeatures: String = "",
      ensembl_host: String  =  "feb2014.archive.ensembl.org" ,
      ensembl_dataset: String  =  "hsapiens_gene_ensembl"  ): (CSV) = {

/* Retrieve known ncRNA annotations and identify neighbouring or overlapping ncRNAs to putative novel miRNAs */

    val for_PD3 =  
        if (knownFeatures == "") {
            // Create reference GTF file. Takes more time!
            REvaluate(
                script = INPUT(path="PDannotations.r"),
                table1 = expression,
                table2 = gtf.asInstanceOf[CSV]
                )
        } else {    
            // Extract known ncRNA positions in genome
            if (new java.io.File(knownFeatures).exists()) {
                REvaluate(
                    script =  INPUT(path="PDannotations.r"),
                    table1 = expression,
                    param1 = knownFeatures
                    )   
            } else {
                sys.error("Input knownFeatures does not exist: " + knownFeatures)
            }
        }

    // Calculate coordinate distance and find nearest neighbour of novel miRNAs     
    val novelExpr_PD3 = PointDistance(
            in = for_PD3.table,
            reference = for_PD3.outArray("novel"),
            inId = "knownID",
            referenceId = "novelID",
            cols = "chr,start,end",
            nth = 2
            )

    // Extract just the best overlapping/neighbouring known ncRNA of novel miRNAs
    val best_PD3 = CSVFilter(
            in = novelExpr_PD3.out,
            highBound = "Distance=1000"
            )

    // Add annotations with expression matrix for putative miRNAs
    // NOTE: Difference between "host" genes and "nearestNCRNA"
    // is that "host" completely overlaps the putative miRNA location,
    // but "nearestNCRNA" is nearby but NOT necessarily overlapping.
    val geneOverlap = REvaluate(
            script = INPUT(path="geneoverlap.r"),
            param1 = ensembl_host,
            param2 = ensembl_dataset,
            //param2 = "/mnt/csc-gc5/icay/_ref/Ensembl37v72/EnsemblGene37v72.txt",
            table1 = expression,
            table2 = best_PD3.out,
            table3 = for_PD3.table,
            table4 = gtf.asInstanceOf[CSV]
            )

    return geneOverlap.table
}