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

[Yue Li]

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.

Thanks much,
Yue