[BioC] how to load RangedData for all chromosomes in one tab in UCSC browser using browserView from rtracklayer

[Steve Lianoglou]

Hi,

On Thu, May 31, 2012 at 1:00 PM, Yue Li <gorillayue at gmail.com> wrote:
> Dear List,
>
> I wonder how to load RangedData for all chromosomes in a SINGLE tab in UCSC browser using browserView from rtracklayer.
>
> Currently, if I have a GRanges object for "mm9" build:
>
>> alignGR
> GRanges with 238161 ranges and 0 elementMetadata cols:
>                    seqnames                 ranges strand
>                       <Rle>              <IRanges>  <Rle>
>  SRR039212.1000031    chr19 [  8790316,   8790351]      -
>  SRR039212.1000085     chr5 [106579844, 106579879]      +
>  SRR039212.1000087     chr8 [109778747, 109778782]      +
>  SRR039212.1000088     chr8 [ 93777537,  93777572]      +
>  SRR039212.1000132     chr3 [128910749, 128910784]      +
>  SRR039212.1000149     chr8 [127433402, 127433437]      +
>  SRR039212.1000170    chr15 [ 93546853,  93546888]      +
>  SRR039212.1000174    chr18 [ 32056273,  32056308]      -
>  SRR039212.1000177     chr7 [ 90292453,  90292474]      -
>                ...      ...                    ...    ...
>   SRR039212.999792     chr2 [162907151, 162907186]      -
>   SRR039212.999805     chr6 [ 44021338,  44021373]      +
>   SRR039212.999810     chr4 [121106682, 121106717]      -
>   SRR039212.999844    chr19 [ 60848841,  60848876]      +
>   SRR039212.999848     chr5 [117644397, 117644432]      -
>   SRR039212.999854     chr6 [132445007, 132445042]      -
>   SRR039212.999855     chr7 [108392362, 108392397]      -
>   SRR039212.999892     chr9 [ 20946884,  20946919]      +
>   SRR039212.999901     chr2 [168845152, 168845187]      +
>  ---
>  seqlengths:
>        chr1     chr10     chr11     chr12     chr13     chr14 ...      chr8      chr9      chrM      chrX      chrY
>   197195432 129993255 121843856 121257530 120284312 125194864 ... 131738871 124076172     16299 166650296  15902555
>
>
> and I do this:
>        session <- browserSession()
>
>
>        track(session, "read alignments") <- RangedData(alignGR)
>
>
>        # launch browser view
>        browserView(session, alignGR)
>
>
>
> This will open 22 tabs in my browser corresponding to 22 chromosomes in the GRanges object. I wonder if it would be possible to have just one single tab open for all 22 chromosomes to view on UCSC browser.

Is there anyway that you know of to have the genome browser do what
you are asking "directly"?

I mean, if you were just navigating w/ the browser alone (not using
rtracklayer), how would you get it to do what you are asking?

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact