rangeColMeans (or rangeMeans) takes a vector, but can recycle over columns in a matrix. I guess we could have rangeMeans for vector-ish things, rangeColMeans and rangeRowMeans for two-d things.
I have rangeMeans for Rles and RleDataFrame, which does each Rle. I'm flexible on naming. Pete ____________________ Peter M. Haverty, Ph.D. Genentech, Inc. phave...@gene.com On Mon, Jun 2, 2014 at 6:50 PM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > 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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