R/GRangesInPromoters.R

In compEpiTools: Tools for computational epigenomics

setGeneric('GRangesInPromoters', function(Object, txdb, upstream=2000,
                                          downstream=1000, invert=FALSE)
  standardGeneric('GRangesInPromoters'))
setMethod('GRangesInPromoters','GRanges', function(Object, txdb,
                                                   upstream=2000, downstream=1000, invert=FALSE) {
  
  if(!is(txdb, "TxDb"))
    stop('txdb has to be of class TxDb ..')
  if(!is.numeric(upstream))
    stop('upstream has to be of class numeric ..')
  if(!is.numeric(downstream))
    stop('downstream has to be of class numeric ..')
  if(!is.logical(invert))
    stop('invert has to be of class logical ...')
  
  suppressWarnings(pregions <- promoters(txdb, upstream=upstream, downstream=downstream, 
                                         columns=c('tx_id','tx_name','gene_id')))
  
  names(pregions) <- pregions$gene_id
  inds <- which(start(pregions)<0)
  if(length(inds)>0) start(pregions)[inds]=1
  
  inds <- overlapsAny(query= Object, subject= pregions)
  if(invert) {
    inds_f <- which(inds==FALSE)
    if(length(inds_f) > 0)
      res <- Object[inds_f]
    else
      res <- NULL
  }
  else {
    inds_t <- which(inds==TRUE)
    if(length(inds_t) > 0) res <- Object[inds_t]
    else res <- NULL
  }
  return(res)
})