On Tue, Jun 30, 2009 at 12:26 AM, Michael Lawrence <mflawren@fhcrc.org>wrote: > > > On Mon, Jun 29, 2009 at 12:22 PM, Paul Shannon < > pshannon@systemsbiology.org> wrote: > >> I used to have a dead-easy way to use rtracklayer to display a new track >> in the UCSC browser: >> >> head (gaps.tsv) # a 6-column tsv file, thus: >> >> name target chrom start end strand >> chr1-0-473 a 1 32 473 + >> chr1-556-587 b 1 556 587 + >> chr1-626-902 c 1 626 902 + >> .... >> tbl = read.table ('gaps.tsv', sep='\t', header=T) >> foo = trackSet (tbl) # the trackSet function no longer available (29 >> jun 2009) >> browseGenome (foo) >> >> With rtracklayer 1.4, trackSet seems to have gone AWOL -- or more likely, >> I have lost my bearings. >> > > Right, rtracklayer is now based on the IRanges infrastructure, rather than > the trackSet class. The trackSet() method for data.frames (which takes the > chrom, start, end, strand, etc automatically), was lost along the way. I > will try to bring something like this back in a future release. > Just checked some stuff into the devel svn. With rtracklayer version 1.5.5, this should be possible: foo <- GenomicData(tbl) > > For now, this will work: > foo <- with(tbl, RangedData(IRanges(start, end), name, target, strand, > space = chrom)) > > Michael > > >> >> I've spent a few hours with the 1.4 vignette, but failed to get my own >> variation on those examples to work. There are quite a few only >> semi-transparent classes involved, and I got lost repeatedly along the way. >> >> Any suggestions for me? I'd like to use rtracklayer. Maybe it will be >> easier to write my own wig file, and upload directly to the UCSC browser... >> >> Cheers, >> >> - Paul >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@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]]