Which step goes from data.frame to RangedData? Setting seqnames as a column
in the RangedData would be an error - that should be encoded as the names()
of the RangedData, i.e., passed as the "space" argument to the constructor.

I'm curious as to why you need to go to data.frame to normalize the data.
RangedData behaves like data.frame in many ways. If something is missing,
please let me know.

Thanks,
Michael

On Tue, Oct 19, 2010 at 1:18 PM, pterry@huskers.unl.edu <
pterry@huskers.unl.edu> wrote:

>  Dear bioc-sig-sequencing,
>
> Following the BioC2010 lab (
> http://www.bioconductor.org/help/course-materials/2010/BioC2010/Workflow.pdf).
>  Would like to coerce GRanges to data.frame form, then to RangedData, and
> finally back to GRanges object (so can normalize number of reads while in
> data.frame form).
>
> GRanges documentation suggests this possible:
>
> ‘as(from, "GRanges")’: Creates a GRanges object from a RangedData or
>          RangesList object.
>
> However, in step from data.frame to RangedData, "seqnames" column placed in
> elementMetadata, and in step from RangedData to GRanges, get error: slot
> 'elementMetadata' now has column named "seqnames".
>
> Can you indicate how to successfully accomplish this set of coercions?
>
> > gr <- as(rd, "GRanges")
> Error in validObject(.Object) :
>  invalid class "GRanges" object: slot 'elementMetadata' cannot use
> "seqnames", "ranges", "strand", "seqlengths", "start", "end", "width", or
> "element" as column names
>
> R version 2.12.0 Under development (unstable) (2010-09-16 r52922)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>  [7] LC_PAPER=en_US.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] BSgenome.Athaliana.TAIR.04232008_1.3.16
>  [2] GenomicFeatures_1.1.12
>  [3] chipseq_0.99.1
>  [4] ShortRead_1.7.21
>  [5] Rsamtools_1.1.15
>  [6] lattice_0.19-11
>  [7] BSgenome_1.17.7
>  [8] Biostrings_2.17.47
>  [9] GenomicRanges_1.1.25
> [10] IRanges_1.7.38
>
> loaded via a namespace (and not attached):
>  [1] Biobase_2.9.2     biomaRt_2.5.1     DBI_0.2-5         grid_2.12.0
>  [5] hwriter_1.2       RCurl_1.4-3       RSQLite_0.9-2
> rtracklayer_1.9.9
>  [9] tools_2.12.0      XML_3.1-1
> >
>
>
> Thanks,
> P. Terry
> pterry@huskers.unl.edu
>
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>
>
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>
>

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