Thanks for pointing this out Steve. I checked in your suggested fix as
version 1.17.17.

Michael

On Mon, Aug 13, 2012 at 4:01 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> I think I must be doing something wrong because whenever I'm using a
> GRanges object to import data from a BigWig, I always end up w/ this
> error:
>
>    'score' is the only valid column for BigWig
>
> Tracing through rtracklayer,bigWig.R it seems that my GRanges object
> is ultimately converted to a BigWigSelection via a few coercions:
> GRanges -> RangesList -> RangedSelection -> BigWigSelection.
>
> Problem is that this creates a "BigWigSelection" object with a
> colnames slot always set to `character()` (from the
> IRanges::RangesList -> RangedSelection step), but really should be
> "score".
>
> One easy fix could be to tweak the coercion method form RangesList to
> BigWigSelection to set the `colnames` slot directly, eg:
>
> setAs("RangesList", "BigWigSelection", function(from) {
>   new("BigWigSelection", as(from, "RangedSelection"), colnames="score")
> })
>
> Not sure if I'm doing something incorrectly, because I imagine this
> bug would have popped up already, but it seems necessary for me to
> tweak rtracklayer like that to get it to work.
>
> If I'm doing something wrong, please let me know.
>
> relevant sessionInfo()
>
> R 2.15.1
> IRanges_1.15.32
> rtracklayer_1.17.16
>
> Thanks,
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>

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