This should be in help(RangedData). On Thu, Jan 26, 2012 at 11:35 AM, Kavitha Mukund <kmukund@ucsd.edu> wrote: > Hello Michael,**** > > Thank you so much! I didn’t know “query[names(subject)]” reorders the > RangedData object - I spent a lot of time trying to reorder the gff file by > converting it into a data frame etc.**** > > Is there a link where this is provided?**** > > Thanks again!**** > > -Kavitha**** > > ** ** > > ** ** > > *From:* Michael Lawrence [mailto:lawrence.michael@gene.com] > *Sent:* Thursday, January 26, 2012 10:59 AM > *To:* Kavitha Mukund > *Cc:* bioconductor@r-project.org > *Subject:* Re: [BioC] Importing error using rtracklayer's "import" > function**** > > ** ** > > ** ** > > On Wed, Jan 25, 2012 at 3:22 PM, Kavitha Mukund <kmukund@ucsd.edu> wrote:* > *** > > Hello, > I am trying to import a gff file from ucsc genome browser using > rtracklayer's "import" function. > Although it imports the file into R without any error, it changes the > order of my chromosomes > > That is to say it is reordering the chromosomes when it inputs into R > genes = import("file.gff") > names(genes)= "chr1" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" > "chr16" "chr17" "chr18" "chr19" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" > "chr8" "chr9" "chrX" "chrY" > > This is giving me some problems when I compute overlaps using > countOverlaps ( IntervalTree-class {IRanges}) as my subject has the order > "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" "chr9" "chr10" > "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" "chr19" > "chrX" "chrY" > > Any advice would be greatly appreciated.**** > > > It's true that rtracklayer current reorders the sequences. That's not very > desirable, so this will be fixed in the next version. To work around this, > simply reorder the RangedData object using query[names(subject)] or similar > to get things in the right order. > > Michael > > **** > > Thanks! > Kavitha > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor**** > > ** ** > [[alternative HTML version deleted]]