[Bioc-devel] as.list of a GRanges

[Hervé Pagès]

Hi Bernat,

Use as(gr, "GRangesList") instead of as.list() on your GRanges objects.

Most of the times (e.g. for passing to lapply() or mclapply()), you
don't need an ordinary list, but, if you really want one, you can call
as.list() on the GRangesList object returned by as(gr, "GRangesList").

Hope this helps,
H.

On 02/15/2018 12:05 AM, Bernat Gel wrote:
> Hi,
> 
> I'm having an error in the devel version of my package karyoploteR due 
> to an error when converting a GRanges into a list of GRanges with 
> "as.list".
> 
> This used to be possible and it was working a few weeks ago.
> 
> Am I suposed to use a different approach or is there a problem somewhere?
> 
> Thanks!
> 
> Bernat
> 
> Here's an example
> 
> rr <- GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(start=c(1, 
> 2), end=c(11, 12)))
> as.list(rr)
> 
> And the error message
> 
> Error in (function (classes, fdef, mtable)  :
>    unable to find an inherited method for function 'getListElement' for 
> signature '"GRanges"'
> 
> 
> and the sessionInfo
> 
>  > sessionInfo()
> R Under development (unstable) (2018-02-14 r74250)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Debian GNU/Linux 8 (jessie)
> 
> Matrix products: default
> BLAS: /software/debian-8/general/R-Bioc-Devel/current/lib/R/lib/libRblas.so
> LAPACK: 
> /software/debian-8/general/R-Bioc-Devel/current/lib/R/lib/libRlapack.so
> 
> locale:
>   [1] LC_CTYPE=en_US.UTF-8      LC_NUMERIC=C LC_TIME=C 
> LC_COLLATE=en_US.utf8
>   [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8 
> LC_PAPER=es_ES.UTF-8      LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C LC_MEASUREMENT=en_US.utf8 
> LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] parallel  stats4    stats     graphics  grDevices utils datasets 
> methods   base
> 
> other attached packages:
> [1] GenomicRanges_1.31.20 GenomeInfoDb_1.15.5 IRanges_2.13.26 
> S4Vectors_0.17.32     BiocGenerics_0.25.3
> 
> loaded via a namespace (and not attached):
> [1] zlibbioc_1.25.0        compiler_3.5.0 XVector_0.19.8 
> tools_3.5.0            GenomeInfoDbData_1.1.0
> [6] RCurl_1.95-4.10        bitops_1.0-6
> 
> 
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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