[BioC] rtracklayer no longer uses TrackSet?
Paul Shannon
pshannon at systemsbiology.org
Mon Jun 29 21:22:19 CEST 2009
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
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