On 02/15/2018 08:37 AM, Michael Lawrence wrote:
So is as.list() no longer supported for GRanges objects? I have found it useful in places.
Very few places. I found a dozen of them in the entire software repo. Now you should use as.list(as(gr, "GRangesList")) instead. as.list() was behaving inconsistently on IRanges and GRanges objects, which is blocking new developments. It will come back with a consistent behavior. More generally speaking IRanges and GRanges will behave consistently as far as their "list interpretation" is concerned. I'll send more details later. H.
On Thu, Feb 15, 2018 at 8:30 AM, Hervé Pagès <hpa...@fredhutch.org <mailto:hpa...@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/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 PagèsProgram 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 <mailto:hpa...@fredhutch.org> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> _______________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=i21ySDBZuY-_wWlEBmfdjm2XPMEHP5PcXGHapMlX2Tw&s=bN6AMFpO0vidOay3ITzHe149LOwS30pooDaVEvIgHKw&e=>
-- 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
