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
[email protected]
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