R/Genome_intervals-coercion-methods.R

In genomeIntervals: Operations on genomic intervals

##' Coercion methods of the genomeIntervals package
##'
##' \describe{
##' \item{coerce}{ This method allows to coerce a
##' \code{\link[genomeIntervals:Genome_intervals_stranded-class]{genomeIntervals
##' object}} into a \code{\linkS4class{GRangesList}} object.}}
##'
##' @aliases coerce,Genome_intervals,GRangesList-method
##' coerce,Genome_intervals,GRanges-method
##' as,Genome_intervals,GRangesList-method
##' as as,Genome_intervals-method
##' @name genomeIntervals coercion methods
##' @rdname Genome_intervals-coercion-methods
##' @param from An object of class \code{\linkS4class{Genome_intervals}}
##' @param to a character string: GRanges or GRangesList
##' @usage \S4method{as}{Genome_intervals}(from,to)
##' @return \describe{
##' \item{coerce}{ A \code{\linkS4class{GRanges}} or \code{\linkS4class{GRangesList}} 
##' containing the result of the coercion.}}
##' @examples
##' \dontrun{
##' annot<-readGff3(system.file("extdata",
##'                             "Dmel-mRNA-exon-r5.52.gff3",
##'                             package="RnaSeqTutorial")
##' gAnnot<-as(annot,"GRangesList") type(annot)
##' }
##' @author Nicolas Delhomme
##' @seealso
##' \itemize{
##' \item \code{\link[genomeIntervals:Genome_intervals_stranded-class]{genomeIntervals
##' object}}
##' \item \code{\link[genomeIntervals:readGff3]{readGff3 function}}
##' }

## coerce into GRanges/List
setAs(from="Genome_intervals",to="GRanges",def=function(from){

  ## first check
  if (!is(from, "Genome_intervals")){stop("'from' must be a Genome_intervals object")}

  ## get all possible gff attributes
  ## to be quick
  ## we expect the types to have the same annotation
  ## so we fetch the first instance of each type and
  ## get the gff attribute names
  ## and use these to get the gffAttributes
  ## and convert that into a df
  mat <- do.call(cbind,lapply(unique(unlist(lapply(
    parseGffAttributes(from[match(unique(as.character(type(from))),type(from))]),
    names))),function(attr,from){
      getGffAttribute(from,attr)
    },from))

  ## create the object
  return(GRanges(ranges=IRanges(
    start=from[,1],
    end=from[,2]),
    seqnames=seqnames(from),
    strand=strand(from),
    cbind(
      DataFrame(apply(
        annotation(from)[!colnames(annotation(from))
                         %in% c("seq_name","strand","gffAttributes")],2,Rle)),
      DataFrame(apply(mat,2,Rle)))
  ))
})


## coerce into
setAs(from="Genome_intervals",to="GRangesList",def=function(from){
  ## create the object
  return(split(as(from,"GRanges"),seqnames(from)))
})