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Question: Reading GFF files into R and GenomeGraphs
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8.9 years ago by
Michael Dondrup140 wrote:
Hi, it took a while to figure out how to read genome annotation files with and without rtracklayer, thanks Michael, and also how to plot bacterial chromosomes using the GenomeGraphs package. I think, this information can be useful for others, so I made a tiny howto. I think some of this could also be added to the documentation examples of the GenomeGraphs package. I would be glad if someone would tell me if that fits or if there are some comments. Thank you again for this package. 1) Howto plot genomic annotation from a GFF file using rtracklayer: require("GenomeGraphs") require("rtracklayer") # read in the gff, example from import.gff: # import a GFF V2 file gff <- import.gff(system.file("tests", "v2.gff", package = "rtracklayer"), version = "2") # the gff object contains an IRanges list with the intervals # we need a function to convert to an AnnotationTrack from an IRanges object: makeAnnotationTrackFromIRanges = function (iranges, dp=DisplayPars(ranges = "yellow", plotId=TRUE )) { iranges.names = if (is.null(names(iranges))) {1:length(iranges)} else {names(iranges)} # make some IDs annotation = data.frame(start=iranges at start, end=iranges at start+iranges@width-1, feature=paste("ranges"), # there is no more feature information here group=c(1:length(iranges)), # put every region in a different group ID=iranges.names) makeAnnotationTrack(regions=annotation, dp=dp) } aTrack = makeAnnotationTrackFromIRanges(gff at ranges[[1]]) # there is a RangesList inside the gff gdPlot(aTrack, minBase=1, maxBase=11000) 2) Howto plot arbitrary chromosome data contained in a data.frame: I wasn't fully content with the output from the import.gff function, I have additional information like gene name & reading frame which I didn't get this way. Assume there is a data.frame "cds" containing annotation with columns containing at least columns: "GeneID", "Start", "Stop" Then, the following function can make an AnnotationTrack from it: makeSingleAnnotationTrack = function (cds, dp=DisplayPars(orf="blue", plotId=T)) { annotation = data.frame(start=cds$Start, end=cds$Stop, feature=rep.int("orf", nrow(cds)), # this can also be taken from some annotation field group=c(1:nrow(cds)), ID=cds\$GeneID ) makeAnnotationTrack(annotation, dp=dp) } 3) Add coverage data to the annotation data: # convert an iranges object into a coverage track # I think this is a bit inefficient for large iranges objects, is there a better way? makeBaseTrackCoverageFromIRanges = function(iranges, ...) { baseCoverage = as.numeric(coverage(iranges)) makeBaseTrack(base=1:length(baseCoverage), value=baseCoverage, ...) } # and then plot this x = IRanges(start=c(2, 0, NA), end=c(NA, NA, 14), width=11:0) plotlist = list(makeAnnotationTrackFromIRanges(x), makeBaseTrackCoverageFromIRanges(x)) gdPlot(plotlist,min=1, max=20) This is maybe not very nice, but hope this helps..... best Michael Am 30.07.2009 um 13:24 schrieb Michael Lawrence: > On Thu, Jul 30, 2009 at 12:52 AM, Michael Dondrup < > Michael.Dondrup at bccs.uib.no> wrote: > >> Dear BioC list, >> >> I'm trying to use the package GenomeGraphs to visualise custom >> genome data >> (genome not in public databases). In the corresponding publication to >> genomegraphs (Durinck et al. BMC Bioinformatics, 2009 ) I found the >> partial >> clue: "... genomic annotation encoded in GFF files can be easily >> used to >> create a custom AnnotationTrack object for visualization... region >> start, >> and end positions need to be given, as well as how these regions >> are to be >> grouped." >> This leaves me with two questions: >> - I have no idea how to parse a GFF file, is there a GFF parser in >> Bioconductor? >> > > Yes, rtracklayer has a parser. Please see the vignette. > > >> >> - If I have such GFF file for a genome, how can I create such an >> AnnotationTrack with all CDS? >> >> Hope somebody can help me with one of this. >> >> Best >> Michael >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
written 8.9 years ago by Michael Dondrup140

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