On Tue, Apr 10, 2012 at 7:00 PM, Dario Strbenac <D.Strbenac@garvan.org.au>wrote:

> I have the latest versions now, but I get a new error message.
>
> > summary(bws[[1]])
>    Length      Class       Mode
>        25 RangedData         S4
> > bws[[1]]
> RangedData with 154014720 rows and 1 value column across 25 spaces
>             space         ranges   |       score
>          <factor>      <IRanges>   |   <numeric>
> 1             chr1     [  1,  20]   |  0.04206303
> 2             chr1     [ 21,  40]   |  0.04206303
> ...            ...            ... ...         ...
> > export.bw(bws[[1]], filename)
> Error in export(rd, con, "BigWig", ...) :
>  error in evaluating the argument 'object' in selecting a method for
> function 'export': Error: object 'rd' not found
>

Ouch, stupid typo, and somehow missed that unit test. Fixed in 1.16.1 (and
devel). You can work around it by simply using export() instead of export.bw,
as long as your file extension is "bw" or "bigWig" (case insensitive).
Otherwise, pass format="bw" to export().


> > sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>  [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] BSgenome.Hsapiens.UCSC.hg18_1.3.17 BSgenome_1.24.0
> [3] Biostrings_2.24.1                  rtracklayer_1.16.0
> [5] GenomicRanges_1.8.3                IRanges_1.14.2
> [7] BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-4.1  RCurl_1.91-1    Rsamtools_1.8.0 stats4_2.15.0
> [5] tools_2.15.0    XML_3.9-4       zlibbioc_1.2.0
>
> ---- Original message ----
> >Date: Tue, 10 Apr 2012 07:07:20 -0700
> >From: Michael Lawrence <lawrence.michael@gene.com>
> >Subject: Re: [BioC] Export a BigWig with rtracklayer
> >To: D.Strbenac@garvan.org.au
> >Cc: bioconductor@r-project.org
> >
> >   On Mon, Apr 9, 2012 at 10:00 PM, Dario Strbenac
> >   <D.Strbenac@garvan.org.au> wrote:
> >
> >     Hello,
> >
> >     I'm having trouble exporting a real-sized BigWig
> >     file. It is of hg18 with a score every 20 bases on
> >     the 25 real chromosomes. It was created from
> >     reading in two different BigWig files, then
> >     subtracting their scores :
> >
> >     score(bws[[1]]) <- score(bws[[2]]) -
> >     score(bws[[1]])
> >
> >     then
> >
> >     export.bw(bws[[1]], filename, "bedGraph",
> >     seqlengths(Hsapiens)[1:25])
> >
> >     After some minutes, I get the error message
> >     Error: serialization is too large to store in a
> >     raw vector
> >
> >     I also tried "auto" for dataFormat. If importing
> >     then exporting a single BigWig without any
> >     modifications to its data, the code works.
> >
> >     What is a better technique ?
> >
> >   Could you please paste the output of sessionInfo()?
> >   It looks like you're using an older version of
> >   rtracklayer, which is very likely broken somehow.
> >
> >   Thanks,
> >   Michael
> >
> >     --------------------------------------
> >     Dario Strbenac
> >     Research Assistant
> >     Cancer Epigenetics
> >     Garvan Institute of Medical Research
> >     Darlinghurst NSW 2010
> >     Australia
> >
> >     _______________________________________________
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>

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