Sounds good. But who is "she"?
On Wed, Jan 22, 2014 at 3:48 PM, Hervé Pagès <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>> 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 42139699d91a34c401eedd36db62716a607d0b06 >> 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> >> mailing list >> 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> >> 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 > [[alternative HTML version deleted]]
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