On Mon, May 10, 2010 at 7:12 PM, Dario Strbenac <D.Strbenac@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
>

	[[alternative HTML version deleted]]

