On 01/22/2014 08:15 PM, Michael Lawrence wrote:
Sounds good. But who is "she"?
we would, she should, she would, we should... that's it! we should... that's what I meant :-b H.
On Wed, Jan 22, 2014 at 3:48 PM, Hervé Pagès <hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>> wrote: On 01/22/2014 03:02 PM, Michael Lawrence wrote: On Wed, Jan 22, 2014 at 1:29 PM, Hervé Pagès <hpa...@fhcrc.org <mailto:hpa...@fhcrc.org> <mailto:hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>>> wrote: Hi Michael, On 01/12/2014 05:16 AM, Michael Lawrence wrote: Hi, It may be time to deprecate the seq*apply family of functions, including seqapply, mseqapply, tseqapply, seqby and seqsplit. These are ancient functions named in referece to the "Sequence" class, now called "Vector". It would seem better for the user to write: asList(lapply(...)) instead of coming up with an alias for that. For readability, we should probably export asList() as an alias for as(x, "List"), which I just cleaned up. Sounds good to me. There is one caveat though: mseqapply has been particularly useful, because it delegates to mapply_List, which is smart enough to handle any vector argument in "...". The mapply,List method of course restricts everything to List. We should probably export mapply_List, probably with a better name. Suggestions? Why do we need all this? Neat. Presumably due to this patch: commit 42139699d91a34c401eedd36db6271__6a607d0b06 Author: maechler <maechler@00db46b3-68df-0310-__9c12-caf00c1e9a41> Date: Wed Nov 28 10:31:42 2012 +0000 mapply(F, <S4>) now works thanks to a version of Herve's patch We should do away with mapply_List now that this is part of released R. Furthermore, maybe she should also remove the mapply() S4 generic from the BiocGenerics package. It's not needed anymore. base::mapply() should work out-of-the-box on any object for which length() and [[ are implemented. H. x <- RleList(11:14, 3:1) Then: > IRanges:::mapply_List(____function(a, b) {a+b}, x, 10) [[1]] numeric-Rle of length 4 with 4 runs Lengths: 1 1 1 1 Values : 21 22 23 24 [[2]] numeric-Rle of length 3 with 3 runs Lengths: 1 1 1 Values : 13 12 11 But also: > base::mapply(function(a, b) {a+b}, x, 10) [[1]] numeric-Rle of length 4 with 4 runs Lengths: 1 1 1 1 Values : 21 22 23 24 [[2]] numeric-Rle of length 3 with 3 runs Lengths: 1 1 1 Values : 13 12 11 What am I missing? Thanks, H. Michael [[alternative HTML version deleted]] ___________________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> <mailto:Bioc-devel@r-project.__org <mailto:Bioc-devel@r-project.org>> mailing list https://stat.ethz.ch/mailman/____listinfo/bioc-devel <https://stat.ethz.ch/mailman/__listinfo/bioc-devel> <https://stat.ethz.ch/mailman/__listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> -- 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...@fhcrc.org <mailto:hpa...@fhcrc.org> <mailto:hpa...@fhcrc.org <mailto:hpa...@fhcrc.org>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> <tel:%28206%29%20667-5791> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> <tel:%28206%29%20667-1319> -- 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...@fhcrc.org <mailto:hpa...@fhcrc.org> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
-- 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...@fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
