[Bioc-devel] as.list of a GRanges

[Michael Lawrence]

So is as.list() no longer supported for GRanges objects? I have found it
useful in places.

On Thu, Feb 15, 2018 at 8:30 AM, Hervé Pagès <hpages at fredhutch.org> wrote:

> 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/li
>> bRblas.so
>> LAPACK: /software/debian-8/general/R-Bioc-Devel/current/lib/R/lib/li
>> bRlapack.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
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>
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