On Fri, Apr 23, 2010 at 2:04 PM, Ivan Gregoretti <[email protected]> wrote:
> Hi all, > > Is it possible to coerce a GRanges to RangedData? > > Apparently, it is not: > > > class(P) > [1] "GRanges" > attr(,"package") > [1] "GenomicRanges" > > as(P,'RangedData') > Error in as(P, "RangedData") : > no method or default for coercing "GRanges" to "RangedData" > > Am I missing a library? > > I just checked one into svn. It behaves mostly as expected. The seqlengths go into the elementMetadata(ranges(rd)). Thank you > > Ivan > > > sessionInfo() > R version 2.12.0 Under development (unstable) (2010-03-25 r51410) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BSgenome.Mmusculus.UCSC.mm9_1.3.16 chipseq_0.3.5 > [3] ShortRead_1.5.21 lattice_0.18-3 > [5] BSgenome_1.15.19 Biostrings_2.15.25 > [7] GenomicRanges_0.0.9 IRanges_1.5.70 > [9] rtracklayer_1.7.11 RCurl_1.3-1 > [11] bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.6.1 grid_2.12.0 hwriter_1.1 tools_2.12.0 XML_2.6-0 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
