On Tue, May 11, 2010 at 1:18 AM, Dario Strbenac <D.Strbenac@garvan.org.au>wrote:

> Thanks, I'm happy to use either way.
>
> Just 1 more question, I now tried to do a simple example with just 1 bigWig
> because it was running slowly, and my example is :
>
> library(rtracklayer)
> library(grDevices)
> session <- browserSession("UCSC")
> track1 <- import("http://129.94.136.7/bw/Bre12p3_MBD2IP_1.bw", selection =
> GenomicSelection("hg18", colnames = "score")) # Using ver. 1.8.1 still.
> track1 <- as(track1, "UCSCData")
> track(session, "Bre12 P3", priority = 1, viewLimits = c(0, 10), color =
> as(col2rgb("green"), "integer")) <- track1
>
> The actual .bw is only 438 Mb, so I'm curious about the resource (memory)
> usage ?
>
>  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
> 10572 darstr    20   0 9375m 9.1g 4876 S    0 57.7  15:26.58 R
>
> It's also curious that processing has stopped at this stage (i.e. I didn't
> get the > prompt yet), because the hard drive is hardly swapping, and I can
> open another R session that goes at 100% CPU (it's run on an 8 core
> computer).
>

Sounds to me like it's network overhead. If the bigWig is 438 MB, then the
wig/bedGraph data is going to be huge. It's important to realize that
rtracklayer does not send tracks to UCSC as bigWig. This is because you need
to give UCSC a URL on a web server. All rtracklayer has is a RangedData
object in memory. Would it be useful for you to have rtracklayer write it
out to some specified location, with a specified URL to pass to UCSC? In
your case, you really only need to pass the URL.

Michael

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