Wonderful. Thanks, Hervé! On 30 August 2016 at 20:45, Hervé Pagès <hpa...@fredhutch.org> wrote: > Hi Pete, > > Thanks for suggesting this fast method. I've formalized this a little > bit by using a generic (identicalVals) + methods. I also tweaked it > in order to avoid false negatives that can occur when 'x' and 'y' have > different names or different seqlevels. So no more fallback to > 'all(x == y)'. > > Committed in SummarizedExperiment 1.3.82. > > BTW please note that 'x == y' and 'identicalVals(x, y)' both ignore > circularity of the underlying sequences e.g. ranges [1, 10] and > [101, 110] represent the same position on a circular sequence of > length 100 so should be considered equal. However for 'x == y' and > 'identicalVals(x, y)', they are not. Something we should address at > some point... > > Cheers, > H. > > > On 08/30/2016 05:57 AM, Peter Hickey wrote: >> >> The cbind,SummarizedExperiment-method checks that the rowRanges slots >> are equal by calling `all(x == x1)`, where x and x1 are GenomicRanges >> objects. This can be kind of slow and makes a large, temporary vector >> when length(x) is large. >> >> I wrote a fast method to check equality of two GenomicRanges objects, >> see https://gist.github.com/PeteHaitch/13787125a165928e652dcfea2a8d166a. >> It takes it from 13.7 seconds to 0.004 seconds for a GenomicRanges >> object with 100M elements on my machine. It uses identical() on key >> slots of the GenomicRanges objects, and I'm not sure if this could >> return false negatives, so I fall back to all(x == x1) if the fast >> method returns FALSE. >> >> Could cbind,SummarizedExperiment-method be updated to use something like >> this? >> >> Cheers, >> Pete >> >> _______________________________________________ >> 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...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319
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