[BioC] no method for coercing S4 class to a vector
Ninni Nahm
ninninahm at gmail.com
Fri Sep 12 15:39:26 CEST 2014
Thank you! That did the trick!
On Fri, Sep 12, 2014 at 2:45 PM, Andrzej Oleś <andrzej.oles at gmail.com>
wrote:
> Dear Ninni,
>
> you probably need to import the 'as.data.frame' method for GRanges
> objects in your NAMESPACE file:
>
> importMethodsFrom(GenomicRanges, as.data.frame)
>
>
> Cheers,
> Andrzej
>
> On Fri, Sep 12, 2014 at 10:27 AM, Ninni Nahm [guest]
> <guest at bioconductor.org> wrote:
> >
> > Dear all,
> >
> > I have a similar problem to this poster here:
> >
> >
> http://grokbase.com/t/r/bioc-devel/141cegqvpf/no-method-for-coercing-this-s4-class-to-a-vector
> >
> > The error message is:
> >
> > Error in as.vector(x) : no method for coercing this S4 class to a vector
> >
> >
> > In my case, however, I'm using the as.data.frame function on a GRanges
> object. When I source my function it works fine, but when I make it into a
> package and then run the function I get the S4 class error.
> >
> > The function seems to be from BiocGenerics:
> >
> >> as.data.frame
> > standardGeneric for "as.data.frame" defined from package "BiocGenerics"
> >
> > function (x, row.names = NULL, optional = FALSE, ...)
> > standardGeneric("as.data.frame")
> > <environment: 0x3801ad8>
> > Methods may be defined for arguments: x
> > Use showMethods("as.data.frame") for currently available ones.
> >
> >
> > So, I have included this
> > importFrom("BiocGenerics", as.data.frame)
> > in NAMESPACE
> >
> > and this
> > Depends: BiocGenerics
> > in DESCRIPTION.
> >
> > It still does not work. I must be missing something.
> >
> > Any help is highly appreciated!
> >
> > Thanks
> > Ninni
> >
> >
> > -- output of sessionInfo():
> >
> >> sessionInfo()
> > R version 3.1.1 (2014-07-10)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods
> > [8] base
> >
> > other attached packages:
> > [1] rtracklayer_1.24.0 GenomicRanges_1.16.2 GenomeInfoDb_1.0.2
> > [4] IRanges_1.22.10 BiocGenerics_0.10.0
> >
> > loaded via a namespace (and not attached):
> > [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.0
> > [4] Biostrings_2.32.0 bitops_1.0-6 brew_1.0-6
> > [7] BSgenome_1.32.0 codetools_0.2-9 DBI_0.2-7
> > [10] digest_0.6.4 fail_1.2 foreach_1.4.2
> > [13] GenomicAlignments_1.0.0 iterators_1.0.7 plyr_1.8.1
> > [16] Rcpp_0.11.1 RCurl_1.95-4.1 Rsamtools_1.16.0
> > [19] RSQLite_0.11.4 sendmailR_1.1-2 stats4_3.1.1
> > [22] stringr_0.6.2 tools_3.1.1 XML_3.98-1.1
> > [25] XVector_0.4.0 zlibbioc_1.10.0
> >
> > --
> > Sent via the guest posting facility at bioconductor.org.
> >
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