R/GenomicAnnotations2GenomicAnnotationsForPREDA.R

In PREDA: Position Related Data Analysis

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## GenomicAnnotations - GenomicAnnotations2GenomicAnnotationsForPREDA
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## Method for class GenomicAnnotations that is actually used only to generate a new GenomicAnnotationsForPREDA object
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setMethod("GenomicAnnotations2GenomicAnnotationsForPREDA", "GenomicAnnotations", function(.Object, positions=NULL, reference_position_type=NULL) {

  if (is.null(positions)) {
  positions<-GenomicAnnotations2reference_positions(.Object, reference_position_type=reference_position_type, withnames=FALSE)
  }

GenomicAnnotationsForPREDA_object<-new("GenomicAnnotationsForPREDA", ids=slot(.Object,"ids"), chr=slot(.Object,"chr"), start=slot(.Object,"start"), end=slot(.Object,"end"), strand=slot(.Object,"strand"), chromosomesNumbers=slot(.Object,"chromosomesNumbers"), chromosomesLabels=slot(.Object,"chromosomesLabels"), position=positions, optionalAnnotations=slot(.Object,"optionalAnnotations"), optionalAnnotationsHeaders=slot(.Object,"optionalAnnotationsHeaders"))

return(GenomicAnnotationsForPREDA_object)

})