1 Jun 2012 01:23
Re: how to load RangedData for all chromosomes in one tab in UCSC browser using browserView from rtracklayer
Not sure if you were asking a question or implying that it's not feasible with UCSC browser. Anyhow, I could just upload to UCSC the bed/bam/bedGraph/gff file containing ranges for multiple chromosomes. Then go to the browser-view to visualize any chromosome in a single window with my browser? On 2012-05-31, at 2:12 PM, Steve Lianoglou wrote: > Hi, > > On Thu, May 31, 2012 at 1:00 PM, Yue Li <gorillayue@...> 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 _______________________________________________ Bioconductor mailing list Bioconductor@... https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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