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

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