Hi,

The GenomicData class does not exist right now. Please try as(cov,
"RangedData").

Michael


On Fri, Mar 13, 2009 at 9:08 AM, <ig2ar-saf2@yahoo.co.uk> wrote:

>
> Hello everybody,
>
> I am trying to somehow visualize how my reads overlap (or cover) mouse
> chr1. A simple concept.
>
> I create a readAlign object like this
>
> aln <- readAlign(sp, myfile, filter = blah)
>
> fine.
>
> Then I compute the coverage like this
>
> cov <- coverage(aln, start=1)[[1]]
>
> fine.
>
> The problem arises when when I try to construct from the coverage:
>
> > gd <- as(cov, "GenomicData")
> Error in as(cov, "GenomicData") :
>  no method or default for coercing "Rle" to "GenomicData"
>
>
> So, basically, I am following Michael's tutorial
>
> http://www.bioconductor.org/workshops/2008/SeattleNov08/rtracklayer/rtracklayer.pdf
>
> Can anybody give me a pointer to figure out why it does not work for me?
>
> Thank you,
>
> Ivan
>
>
>
> > sessionInfo()
> R version 2.9.0 Under development (unstable) (2009-03-10 r48103)
> x86_64-unknown-linux-gnu
>
> locale:
>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] rtracklayer_1.3.9                  RCurl_0.94-1
>  [3] org.Mm.eg.db_2.2.6                 RSQLite_0.7-1
>  [5] DBI_0.2-4                          AnnotationDbi_1.5.18
>  [7] Biobase_2.3.10                     BSgenome.Mmusculus.UCSC.mm9_1.3.11
>  [9] ShortRead_1.1.43                   lattice_0.17-20
> [11] BSgenome_1.11.13                   Biostrings_2.11.40
> [13] IRanges_1.1.48
>
> loaded via a namespace (and not attached):
> [1] grid_2.9.0  hwriter_1.1 XML_2.3-0
>
>
>
>
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>

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