So rangeMeans,matrix implies rangeColMeans? Honestly, I would just have a rangeColMeans and rangeRowMeans, which is consistent with the existing row/colMeans. Don't see a good reason to prefer columns over rows.
On Mon, Jun 2, 2014 at 5:34 PM, Peter Haverty <haverty.pe...@gene.com> wrote: > I have have rangeColMeans which is essentially rangeMeans for > vector/matrix. I renamed this to make it a method on rangeMeans. I think it > would be great to have methods for all the commonly used types. We should > put some thought into how these would all share as much code as is > practical. > > Pete > > ____________________ > Peter M. Haverty, Ph.D. > Genentech, Inc. > phave...@gene.com > > > On Mon, Jun 2, 2014 at 1:24 PM, Michael Lawrence < > lawrence.mich...@gene.com> wrote: > >> While we rework things, what about adding support for atomic vectors, in >> addition to Rles? Also, what about functions that are optimized for >> partitionings? Those would be easy to write and would let us greatly >> accelerate e.g. sum,CompressedIntegerList. Right now we rely on rowsum() >> which is fast but could be much faster. >> >> Michael >> >> >> >> On Mon, Jun 2, 2014 at 10:48 AM, Hervé Pagès <hpa...@fhcrc.org> wrote: >> >>> Hi Peter, >>> >>> Seems like you have a pretty good implementation of the view* functions >>> in genoset. Nice work! And great to hear that there is so much room for >>> improvements to the implementation currently in IRanges. I'll try to >>> give this a shot soon but first I want to move Rle's to the S4Vectors >>> package. >>> >>> Cheers, >>> H. >>> >>> >>> >>> On 06/01/2014 07:58 PM, Peter Haverty wrote: >>> >>>> I think viewMedians would be great. While you have the hood up, there >>>> are >>>> some opportunities for some speedups and code simplification, I believe. >>>> >>>> I did some experimentation with view* in the genoset package. I made an >>>> alternate version of the C for viewMeans and found about a 10X speedup. >>>> I >>>> hoisted the branching for the different types and did the NA handling >>>> with >>>> arithmetic rather than branching. The search for the Rle runs covered by >>>> each view is now done with findInterval. There are quite a few code >>>> sections that differ only in the type of the NA value and the pointers >>>> to >>>> the input/output vectors. I think it would be worth considering C++ >>>> templates. >>>> >>>> On the R side, each view* function is pretty similar too. In >>>> genoset/R/RleDataFrame-views.R I tried to factor out all the shared >>>> pieces. >>>> >>>> While we're on the topic, I think the view* functions should have range* >>>> equivalents that skip the View object and work on an Rle and an IRanges. >>>> If you already have a Views object around, view* are perfect. >>>> Otherwise, >>>> making the Views objects uses time that could be saved. >>>> >>>> Overall I found about a 90X speedup over viewMeans(RleViewsList). >>>> >>>> I hope there is some useful food for thought in these experiments. I >>>> have a >>>> vignette that shows some of the timings if anyone is interested. >>>> >>>> Regards, >>>> Pete >>>> >>>> ____________________ >>>> Peter M. Haverty, Ph.D. >>>> Genentech, Inc. >>>> phave...@gene.com >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> 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 >>> Phone: (206) 667-5791 >>> Fax: (206) 667-1319 >>> >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> > [[alternative HTML version deleted]]
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