[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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