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
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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