Hi Steve,

It seems to be working in my heavily hacked version. Btw, you can pass
"range = gr" directly to import.bw, without creating the BigWigSelection
object.

Michael

On Thu, Feb 23, 2012 at 8:07 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> I've been chasing my tail for a while on this -- I'm trying to import
> some data from a bigWig files using R-2.14 and R-devel.
>
> Seems like mostly-current R-devel + bioc packages isn't happy for some
> reason.
>
> Consider this snipped using R-2.14 on a BigWigFile object of interest:
>
> R> import.bw(bwf, BigWigSelection(GRanges("chrX_random",
> IRanges(104857,104931))))
> RangedData with 75 rows and 1 value column across 1 space
>          space           ranges   |     score
>       <factor>        <IRanges>   | <numeric>
> 1   chrX_random [104857, 104857]   |    -0.424
> 2   chrX_random [104858, 104858]   |     0.971
> 3   chrX_random [104859, 104859]   |     1.381
> 4   chrX_random [104860, 104860]   |     2.146
> 5   chrX_random [104861, 104861]   |     4.665
> 6   chrX_random [104862, 104862]   |     3.966
> 7   chrX_random [104863, 104863]   |     1.012
> 8   chrX_random [104864, 104864]   |     4.161
> 9   chrX_random [104865, 104865]   |     2.412
> ...         ...              ... ...       ...
>
> Same file, same selection using R-devel
>
> R> import.bw(bwf, BigWigSelection(GRanges("chrX_random",
> IRanges(104857,104931))))
> RangedData with 75 rows and 0 value columns across 1 space
>          space           ranges   |
>       <factor>        <IRanges>   |
> 1   chrX_random [104857, 104857]   |
> 2   chrX_random [104858, 104858]   |
> 3   chrX_random [104859, 104859]   |
> 4   chrX_random [104860, 104860]   |
> 5   chrX_random [104861, 104861]   |
> 6   chrX_random [104862, 104862]   |
> 7   chrX_random [104863, 104863]   |
> 8   chrX_random [104864, 104864]   |
> 9   chrX_random [104865, 104865]   |
> ...         ...              ... ...
>
> Strangely a call to `summary` works in R-devel and gives the same
> result as it does in R-2.14:
>
> R> summary(bwf, GRanges("chrX_random", IRanges(104857,104931)))
> SimpleRleList of length 1
> [[1]]
> 'numeric' Rle of length 1 with 1 run
>  Lengths:                1
>  Values : 2.46041230119978
>
>
> This is my sesionInfo for R-devel:
>
> R Under development (unstable) (2011-11-04 r57571)
> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rtracklayer_1.15.7   GenomicRanges_1.7.26 IRanges_1.13.24
> [4] BiocGenerics_0.1.4
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.23.6 bitops_1.0-4.1    BSgenome_1.23.2   RCurl_1.91-1
> [5] Rsamtools_1.7.35  tools_2.15.0      XML_3.6-2         zlibbioc_1.1.0
>
>
> --
> 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
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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