On Fri, Jul 3, 2009 at 5:34 AM, Robert Castelo <robert.castelo@upf.edu>wrote:

> dear list,
>
> i'd like to know how can i download the conservation track for several
> genomic ranges belonging to different chromosome sequences


This is not supported yet, mostly because whenever people have multiple
regions, they have a lot of regions, and the current, simple implementation
would be too slow. It is possible though to upload a track to UCSC and ask
it for the regions that intersect that track. I'll put that on the TODO
list; actually it was already on there. For now, you might just have to loop
in R and make separate requests.


> as the
> example below seems only to retrieve this information for 1 of the
> chromosomes, (the first one on the list):
>
> library(rtracklayer)
>
> session <- browserSession("UCSC")
>
> genome(session) <- "hg18"
>
> track(session, "Conservation",
> GenomicRanges(start=c(27099139,52708461,32260488),end=c(27102150,52710874,32265941),chrom=c("chr7","chr12","chr6"),
> genome="hg18"))
> UCSC track 'Primate Cons'
> UCSCData: 3012 ranges by 1 columns
> columns(1): score
> sequences(1): chr7
>
> thanks!
> robert.
>
> sessionInfo()
> R version 2.9.1 (2009-06-26)
> x86_64-unknown-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] rtracklayer_1.4.1 RCurl_0.98-1      bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] BSgenome_1.12.2   Biobase_2.4.1     Biostrings_2.12.7
> IRanges_1.2.3
> [5] XML_2.5-3
>
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