On Thu, May 6, 2010 at 7:31 PM, Dario Strbenac <D.Strbenac@garvan.org.au>wrote:

> Thanks for these tips.
>
> Just another problem, however. I'm having trouble loading in the tracks.
> I've tried copying the file to my hard drive and also using it from another
> computer on the network.
>
> # Try 1
> library(rtracklayer)
> track1 <- import("C:/Users/dario/Documents/Garvan/Bre12p3_MBD2IP_1.bw")
>
> # Try 2
> library(rtracklayer)
> track1 <- import("http://129.94.136.7/bw/Bre12p3_MBD2IP_1.bw")
>
> I killed both processes after 10 minutes. They each use 100% of 1 CPU.
> Could that mean an infinite loop somewhere ? I have also tried out other
> bigWigs, and it's the same result.
>
> Could you try to replicate the '# Try 2' snippet please ? The file should
> be web - accessible.
>
> I am using version 1.8.1 of the package and 2.11.0 R (for 64 bit Windows
> edition).
>
>
It seems to work fine on my Linux machine. I have never tested the bigwig
support on Windows, and I'm not surprised that it's broken. The UCSC library
that I use to parse them is not supported on Windows. I managed to hack it
to get it to compile, but it's probably not close to working. Developing on
Windows is a pain.

If you have access to a Linux or Mac, give it a try. Note that for bigwig,
since we're usually dealing with big files, you're expected to give it some
notion of what you want out of the file. So you'll need something like:

track1 <- import("http://129.94.136.7/bw/Bre12p3_MBD2IP_1.bw", selection =
GenomicSelection("hg19"))

To get the whole file, if it's for the hg19 genome. See BigWigSelection and
GenomicSelection for more details.



> Thanks.
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>

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