[BioC] rtracklayer GraphTrackLine

[Dario Strbenac]

Ah, right. I did a bit of inversigating, and I think it doesn't seem to like BigWigs. Here's my reproducible example :

library(rtracklayer)
track1 <- import("http://129.94.136.7/bw/Bre12p3_MBD2IP_1.bw", selection = GenomicSelection("hg18"))

> track1 at values$chr1
DataFrame with 2928039 rows and 0 columns

I don't think there would be a problem with the .bw file being corrupted or anything. We've seen it in UCSC browser before and it looks good.

Thanks,
       Dario.

---- Original message ----
>Date: Mon, 10 May 2010 19:25:50 -0700
>From: Michael Lawrence <lawrence.michael at gene.com>  
>Subject: Re: [BioC] rtracklayer GraphTrackLine  
>To: D.Strbenac at garvan.org.au
>Cc: Michael Lawrence <lawrence.michael at gene.com>, bioconductor at stat.math.ethz.ch
>
>   On Mon, May 10, 2010 at 7:12 PM, Dario Strbenac
>   <D.Strbenac at garvan.org.au> wrote:
>
>     Hello again,
>
>     I'm really close to having it all working now.
>     It's just that when I try to pass some parameters
>     to track() that you'd expect to be available, they
>     don't seem to.
>
>     e.g.
>
>     > track(session, "Bre12 P3", priority = 1,
>     viewLimits = c(0, 10), color =
>     as(col2rgb("green"), "integer")) <- track1
>
>     Error in .local(object, con, variant, color,
>     append, ...) :
>      unused argument(s) (viewLimits = c(0, 10))
>
>     Is this something that is still in development
>     perhaps ?
>
>   This is not a fully reproducible example, but my
>   guess is that your 'track1' does not have a numeric
>   "score" column. Thus, rtracklayer assumes you want
>   to upload it as a BED track rather than as a graph
>   track (either wig or bedGraph, depending on some
>   complex logic). In that case, the graph-specific
>   parameters are invalid.
>
>   You can check this by calling as(track1, "UCSCData)
>   and then checking the class of the 'trackLine' slot.
>   To force the use of wig/bedGraph, simply pass
>   format="wig" or format="bedGraph" to the track<-
>   function.
>
>   Michael
>    
>
>     Thanks,
>           Dario


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