[Bioc-devel] writeVcf performance

Hi guys (Val, Martin, Herve): Anyone have an itch for optimization? The writeVcf function is currently a bottleneck in our WGS genotyping pipeline. For a typical 50 million row gVCF, it was taking 2.25 hours prior to yesterday's improvements (pasteCollapseRows) that brought it down to about 1

Re: [Bioc-devel] Additional summarizeOverlaps counting modes for ChIP-Seq

Hi Valerie, I got really busy around May and never got a chance to thank you for adding this option to summarizeOverlaps! So thank you! -Ryan On Thu 01 May 2014 04:25:33 PM PDT, Valerie Obenchain wrote: GenomicAlignments 1.1.8 has a 'preprocess.reads' argument. This should be a function

Re: [Bioc-devel] Additional summarizeOverlaps counting modes for ChIP-Seq

Hi again, I'm looking at the examples in the summarizeOverlaps help page here: http://www.bioconductor.org/packages/devel/bioc/manuals/GenomicAlignments/man/GenomicAlignments.pdf And the examples fod preprocess.reads are a little confusing. One of the examples passes some additional ...

[Rd] Minor documentation change for assign

Good afternoon, Today I was reading the documentation , | help('-'); ` . The passage (I added the asterisks) The operators '' are normally only used in functions, and cause a search *to* made through parent environments for an existing definition of the variable being

[Rd] Is it a good idea or even possible to redefine attach?

Hi, Today I got curious about whether or not I /could/ remove `attach' from my system so: - Backed it up - Implemented a new one - Like this , | attach.old - attach | attach - function(...) {stop(NEVER USE ATTACH)} ` I got the error: , | Error: cannot change value of locked binding

Re: [Rd] Is it a good idea or even possible to redefine attach?

On Tue, Aug 5, 2014 at 2:49 PM, Grant Rettke g...@wisdomandwonder.com wrote: Hi, Today I got curious about whether or not I /could/ remove `attach' from my system so: - Backed it up - Implemented a new one - Like this , | attach.old - attach | attach - function(...) {stop(NEVER USE

Re: [Rd] Is it a good idea or even possible to redefine attach?

On Tue, Aug 5, 2014 at 1:49 PM, Grant Rettke g...@wisdomandwonder.com wrote: Hi, Today I got curious about whether or not I /could/ remove `attach' from my system so: - Backed it up - Implemented a new one - Like this , | attach.old - attach | attach - function(...) {stop(NEVER USE

Re: [Rd] Is it a good idea or even possible to redefine attach?

That is delightful. When I run it like this: • Start R • Nothing in .Rprofile • Paste in your code ╭ │ gcrenv - new.env() │ gcrenv$attach.old - attach │ gcrenv$attach - function(...){stop(NEVER USE ATTACH)} │ base::attach(gcrenv, name=gcr, warn.conflicts = FALSE) ╰ • I get exactly what is

[Rd] More than one package document with the same name

Hi, I sent this to the Bioconductor mailing list (q.v.), replies recommended this forum. Here it is: A suggestion. Typically a package provides documentation of two types, one or more vignettes and a reference manual; and they have the same file name, PackageName.pdf. When downloaded some

Re: [Rd] More than one package document with the same name

On Tue, Aug 5, 2014 at 5:47 PM, Davison, Jerry jdavi...@fhcrc.org wrote: Hi, I sent this to the Bioconductor mailing list (q.v.), replies recommended this forum. Here it is: A suggestion. Typically a package provides documentation of two types, one or more vignettes and a reference manual;

Re: [Rd] Is it a good idea or even possible to redefine attach?

On Tue, Aug 5, 2014 at 4:37 PM, Grant Rettke g...@wisdomandwonder.com wrote: That is delightful. When I run it like this: • Start R • Nothing in .Rprofile • Paste in your code ╭ │ gcrenv - new.env() │ gcrenv$attach.old - attach │ gcrenv$attach - function(...){stop(NEVER USE ATTACH)}