On Wed, May 5, 2010 at 5:32 PM, Dario Strbenac <D.Strbenac@garvan.org.au>wrote:

> Hello,
>
> I'm running into difficulties into converting my track into a
> GraphTrackLine. I assume this is what I need to do next ?
>
> > library(rtracklayer)
> Loading required package: RCurl
> Loading required package: bitops
> > track1 <- import("myFolder/MBD2IP_1.bw")
> > track1 <- as(track1, "GraphTrackLine")
> Error in as(track1, "GraphTrackLine") :
>  no method or default for coercing "RangedData" to "GraphTrackLine"
>
>
You can convert your track to a UCSCData object, which has a trackline. The
track itself cannot be represented by a single line. A lot of times, you
don't even need to worry about this. For example, if you want to upload the
track to the UCSC browser, you can specify track line parameters in the call
to the track<- function. See the "Plotting the SNP track" example in the
vignette.


> I am aiming to convert it into a GraphTrackLine object so that I can set
> the viewLimits, color, etc. slots and then visualise it programatically with
> browserView() across about 100 windows.
>
> I also read about some wigTrackLine class in the user manual, and thought
> maybe that's what I need to use, but it seems not to exist anymore ?
>
>
Right the wigTrackLine has been replaced by the GraphTrackLine class. I'll
fix the documentation.

Thanks,
Michael



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