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
>>
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>
>

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