On Fri, Mar 5, 2010 at 4:32 PM, Wu, Xiwei <XWu@coh.org> wrote:

> Hi,
>
> I recently started to use rtracklayer, so I am still new to it. Here I
> am trying to get conservation score for a number of genomic loci. The
> code below works, but extremely slow. I found it took several seconds to
> get one done, so it becomes impossible when it gets to over 1000 sites.
> What is missing here? Is there any alternative way to get this done? Any
> help will be highly appreciated.
>
>
Each query will result in several HTTP requests. If you're going to be
accessing conservation often, you could download the track, convert it to
bigWig and use the bigWig import support.

At some point it might make sense to get the conservation track into some
sort of R package for distribution.

I'm also working on getting the intersection support working in the table
browser. Just another thing on the TODO list.

Michael

> head(dum)
>   chr     start       end
> 1 chr1   7233717   7233734
> 2 chr1  48238854  48238870
> 3 chr1 175465350 175465366
> 4 chr1 206969193 206969209
> 5 chr1 214532960 214532976
> 6 chr1 216671605 216671622
>
> > getConserv <- function(genome="hg18", data) {
> +       session <- browserSession()
> +       result <- numeric()
> +       genome(session) <- genome
> +       for (i in 1:nrow(data)) {
> +               query <- ucscTableQuery(session,
> "cons44way",GenomicRanges(data[i,"start"]), data[i, "end"],
> data[i, "chr"]))
> +               tableName(query) <- "phyloP44wayPlacMammal"
> +               a <- track(query)
> +               result[i] <- mean(score(a))
> +       }
> +       return(result)
> + }
> > b <- getConserv(data=dum)
> > head(b)
> [1] -1.76180289 -0.28795906  0.05897465 -0.23541347 -0.26477671
> 0.29019661
>
>
> > sessionInfo()
> R version 2.11.0 Under development (unstable) (2010-01-28 r51065)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> other attached packages:
>  [1] rtracklayer_1.6.0                  RCurl_1.3-1
>
>  [3] bitops_1.0-4.1                     smRNAseq_1.0
>
>  [5] time_1.0
> BSgenome.Hsapiens.UCSC.hg18_1.3.16
>  [7] ShortRead_1.5.11                   lattice_0.18-3
>
>  [9] BSgenome_1.15.4                    Biostrings_2.15.19
>
> [11] IRanges_1.5.36
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.7.4 grid_2.11.0   hwriter_1.1   tools_2.11.0  XML_2.6-0
>
> Xiwei
>
>
> ---------------------------------------------------------------------
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>
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