rtracklayer no longer uses TrackSet?
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Paul Shannon ★ 1.1k
@paul-shannon-578
Last seen 7.9 years ago
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. 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
rtracklayer rtracklayer • 585 views
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@michael-lawrence-2759
Last seen 7.9 years ago
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. 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]]
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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]]
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