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Viewing changes to R/methods-CuffGene.R

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-12-28 17:17:25 UTC
  • mfrom: (1.1.2)
  • Revision ID: package-import@ubuntu.com-20131228171725-polmzo8go4m371c6
Tags: 2.4.1-1
* New upstream version
* debian/rules: Remove useless creation of ${R-Depends}
* debian/control: Versioned Build-Depends: r-base-dev (>= 3.0)
* debian/README.test: add hint how to test the package

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R/methods-CuffGene.R
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#################
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#Validate               #
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#################
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#TODO: Add validity constraints
 
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setValidity("CuffGene",function(object){
 
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                        objLen = length(object)
 
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                        if(objLen==0){
 
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                                write("No gene set returned (Gene might not be in database?)",stderr())
 
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                                return(FALSE)
 
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                        }
 
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                        if(objLen>1){
 
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                                write("Warning: Possibly more than one gene returned",stderr())
 
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                                return(TRUE)
 
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                        }
 
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                }
 
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)               
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#################
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#Class Methods  #
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#################
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setMethod("show","CuffGene",function(object){
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                cat(class(object),"instance for gene",object@id,"\nShort name:\t",unique(object@annotation$gene_short_name),
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                                                "\nSlots:\n\t annotation\n\t fpkm\n\t diff\n\t",
 
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                                                "\nSlots:\n\t annotation\n\t features\n\t fpkm\n\t repFpkm\n\t diff\n\t count\n\t",
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                                                "isoforms\t",class(object@isoforms),"instance of size",length(object@isoforms),"\n\t",
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                                                "TSS\t\t",class(object@TSS),"instance of size",length(object@TSS),"\n\t",
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                                                "CDS\t\t",class(object@CDS),"instance of size",length(object@CDS),"\n"
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                }
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)
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setMethod("length","CuffGene",
 
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                function(x){
 
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                        dim(x@annotation)[1]
 
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                }
 
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)
 
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#################
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#Subsetting             #
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#################
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                        return(object@relCDS)
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                })
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#features
 
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setMethod("features","CuffGene",function(object){
 
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                        return(object@features)
 
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                })
 
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#################
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#Plotting               #
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#################
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#################
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#Misc                   #
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#################
 
 
b'\\ No newline at end of file'
 
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.makeGeneRegionTrack<-function(object){
 
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        featCols<-c('seqnames','start','end','source','gene_id','exon_number','isoform_id','isoform_id','exon_number','strand')
 
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        feats<-features(object)[,featCols]
 
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        newColnames<-c('seqnames','start','end','feature','gene','exon','transcript','symbol','rank','strand')
 
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        mychr<-unique(feats$seqnames)
 
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        colnames(feats)<-newColnames
 
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        feats<-feats[,-1]
 
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        #print(feats)
 
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        feats$symbol[is.na(feats$symbol)]<-"NA"
 
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        #THIS NEEDS TO BE MADE GENERIC
 
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        genetrack<-GeneRegionTrack(feats,genome=object@genome,chromosome=mychr,name='CuffDiff',showId=T,stacking="pack")
 
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        genetrack
 
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}
 
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setMethod("makeGeneRegionTrack",signature(object="CuffGene"),.makeGeneRegionTrack)
 
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.plot<-function(object){
 
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        trackList<-list()
 
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        myStart<-min(object@features$start)
 
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        myEnd<-max(object@features$end)
 
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        #Make the following conditional on network connectivity
 
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        ideoTrack <- IdeogramTrack(genome = object@genome, chromosome = unique(object@features$seqnames))
 
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        trackList<-c(trackList,ideoTrack)
 
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        axtrack<-GenomeAxisTrack()
 
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        trackList<-c(trackList,axtrack)
 
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        genetrack<-.makeGeneRegionTrack(object)
 
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        trackList<-c(trackList,genetrack)
 
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        biomTrack<-BiomartGeneRegionTrack(genome=object@genome,chromosome=as.character(unique(object@features$seqnames)),start=myStart,end=myEnd,name="ENSEMBL",showId=T)
 
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        trackList<-c(trackList,biomTrack)
 
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        plotTracks(trackList,from=myStart-2000,to=myEnd+2000)
 
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}
 
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setMethod("genePlot",signature(object="CuffGene"),.plot)
 
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#################
 
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#Coersion methods
 
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#################
 
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#As GRanges
 
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.asGRanges<-function(object){
 
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        #featCols<-c('seqnames','start','end','source','gene_id','exon_number','isoform_id','isoform_id','exon_number','strand')
 
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        feats<-object@features
 
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        #newColnames<-c('seqnames','start','end','feature','gene','exon','transcript','symbol','rank','strand')
 
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        colnames(feats)[colnames(feats)=='isoform_id']<-'transcript'
 
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        colnames(feats)[colnames(feats)=='gene_id']<-'gene'
 
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        colnames(feats)[colnames(feats)=='exon_number']<-'exon'
 
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        colnames(feats)[colnames(feats)=='source']<-'feature'
 
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        feats$symbol<-feats$transcript
 
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        corCols<-c('seqnames','start','end','strand')
 
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        myGR<-GRanges(Rle(feats$seqnames),ranges=IRanges(feats$start,end=feats$end),strand=Rle(feats$strand),elementMetadata=feats[,!colnames(feats) %in% corCols])
 
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        myGR
 
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}
 
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#As GRangesList
 
 
b'\\ No newline at end of file'