R/reverse.R

In NoRCE: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

commonGene <- function(mrnaobject,
                       org_assembly,
                       downstream,
                       upstream,
                       inputGene,
                       inGeneType) {
  a <- unique(unlist(mrnaobject@geneList))
  aa <-
    convertGeneID(genelist = a,
                  genetype = 'NCBI',
                  org_assembly = org_assembly)
  
  a1 <- convertGeneID(genelist = inputGene,
                      genetype = inGeneType,
                      org_assembly = org_assembly)
  
  big_islands <-
    resize(a1, width = upstream + width(a1), fix = "start")
  hits <- findOverlaps(big_islands, aa, ignore.strand = TRUE)
  tmp <- big_islands[S4Vectors::queryHits(hits), ]
  tmp1 <- aa[S4Vectors::subjectHits(hits), ]
  pairss <- data.frame(tmp$gene, tmp1$gene)
  
  big_islands <-
    resize(a1, width = downstream + width(a1), fix = "end")
  hits <- findOverlaps(big_islands, aa, ignore.strand = TRUE)
  tmp <- big_islands[S4Vectors::queryHits(hits), ]
  tmp1 <- aa[S4Vectors::subjectHits(hits), ]
  
  pairss <- rbind(pairss, data.frame(tmp$gene, tmp1$gene))
  
  getNoncode <- function(x) {
    a <-
      pairss[which(pairss[, 2] %in% unlist(mrnaobject@geneList[[x]])), 1]
    a[!duplicated(a)]
  }
  
  ab <- lapply(seq_along(mrnaobject@Term), getNoncode)
  
  ab[IRanges::isEmpty(ab)] <- 'NA'
  if (length(mrnaobject@geneList) == 1)
    ab <- list(ab)
  return(ab)
}