Re: [Bioc-devel] is.unsorted method for GRanges objects

OK. Thanks Pete for the timings. The fact that the relative difference in speed is larger for small n in your brief tests is because one performs roughly in n*log(n) (quicksort-based) and the other one is linear in time. Which is why I assumed (but without doing any testing) that the latter was go

Re: [Bioc-devel] is.unsorted method for GRanges objects

Thanks for everyones' input. @Hervé FWIW, the below benchmark suggests that unfortunately this is a fair bit slower than is.unsorted(order(gr)) when the length of the GRanges object is < 10,000,000 (the relative difference in speed is larger for small n in my brief tests; I didn't check above n >

Re: [Bioc-devel] BiocStyle::doc_date() not found when testing on Travis via metacran/r-builder

I should add that in my local machine I have pandoc 1.13.1 installed. Also, I just noted that metacran/r-builder uses pandoc 1.12.4.2 at https://github.com/metacran/r-builder/blob/master/pkg-build.sh#L17 So this could be a pandoc issue. On Mon, Nov 2, 2015 at 11:07 PM, Leonardo Collado Torres wr

[Bioc-devel] BiocStyle::doc_date() not found when testing on Travis via metacran/r-builder

Hi, I was going to ask this as an issue at the Bioconductor/BiocStyle repo, but the issue tracker is disabled. I ran into a bug which I'm not sure where it comes from. It happens during R CMD build using BiocStyle to generate an html vignette. For example, here is one such error: Quitting from line

Re: [Bioc-devel] is.unsorted method for GRanges objects

On Mon, Nov 2, 2015 at 6:39 PM, Hervé Pagès wrote: > Hi, > > @Pete: > > 2a- I would just compare pairs of adjacent elements, taking > advantage of the fact that <= is vectorized and cheap. So something > like: > > setMethod("is.unsorted", "Vector", > function(x, na.rm=FALSE, strictly=FALSE)

Re: [Bioc-devel] is.unsorted method for GRanges objects

Hi, @Pete: 2a- I would just compare pairs of adjacent elements, taking advantage of the fact that <= is vectorized and cheap. So something like: setMethod("is.unsorted", "Vector", function(x, na.rm=FALSE, strictly=FALSE) { if (length(x) <= 1L) return(FALSE)

Re: [Bioc-devel] is.unsorted method for GRanges objects

genoset has an is.unsorted for GenomicRanges. I profiled a bit and found a pretty quick way to do it. My version ignores strand, so it is only proper in some cases. But, maybe it's a head start on a fully general function. Pete Peter M. Haverty, Ph.D. Genentech, Inc. phave.

Re: [Bioc-devel] is.unsorted method for GRanges objects

The notion of sortedness is already formally defined, which is why we have an order method, etc. The base is.unsorted implementation for "objects" ends up calling base::.gt() for each adjacent pair of elements, which is likely too slow to be practical, so we probably should add a custom method. T

Re: [Bioc-devel] Idea for improved visibility of Bioconductor packages

- Original Message - > From: "Jiří Hon" > To: "bioc-devel" > Sent: Thursday, October 29, 2015 7:05:57 AM > Subject: Re: [Bioc-devel] Idea for improved visibility of Bioconductor > packages > The implementation of Open Graph protocol should solve this, at least > for LinkedIn and Faceb

Re: [Bioc-devel] is.unsorted method for GRanges objects

Pete, What does sorted mean for granges? If the starts are sorted but the ends aren't does that count? What if only the ends are but the ranges are on the negative strand? Do we consider seqlevels to be ordinal in the order the levels are returned from seqlevels ()? That usually makes sense, but

[Bioc-devel] is.unsorted method for GRanges objects

Hi all, I sometimes want to test whether a GRanges object (or some object with a GRanges slot, e.g., a SummarizedExperiment object) is (un)sorted. There is no is.unsorted,GRanges-method or, rather, it defers to is.unsorted,ANY-method. I'm unsure that deferring to the is.unsorted,ANY-method is what

[Bioc-devel] FW: [bioc] A: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for

Valerie, Could you please help answer the multicore problem the user experienced with? FYI, I used parLapply to replace lapply when multicore = TRUE. Thanks! Best regards, Julie From: "alexgraehl [bioc]" mailto:nore...@bioconductor.org>> Reply-To: "reply+c798347e+c...@bioconductor.org