[Bioc-devel] Restrictions on findOverlaps parameters with SummarizedExperiment objects

2014-04-10 Thread Peter Hickey
Could the findOverlaps method with signatures involving SummarizedExperiment objects please be extended to allow the full range of "type" and "select" arguments"? Please see the examples below for situations where the parameter choices seem unduly restrictive. Are there reasons for these restric

Re: [Bioc-devel] Dependency on windowing systems in the flowCore package

2014-04-10 Thread Kieran O'Neill
Thanks Kevin! That would have been my proposed option 3 if I had realised it would be that simple. This will make my (and several other analysts I know's) lives a lot easier! Cheers, Kieran On 10 April 2014 16:11, Kevin Ushey wrote: > Hi Kieran, > > I've kickstarted the process by sending

Re: [Bioc-devel] compare generics

2014-04-10 Thread Hervé Pagès
Hi Laurent, On 04/09/2014 12:36 PM, Laurent Gatto wrote: Dear all, What are your thoughts about adding a new generic to BiocGenerics: setGeneric("compare", function(x, y, ...) setGeneric("compare")) I have spotted a couple of existing cases on CRAN (lava (S3) and NMF (S4) with signature fu

Re: [Bioc-devel] Dependency on windowing systems in the flowCore package

2014-04-10 Thread Kevin Ushey
Hi Kieran, I've kickstarted the process by sending a pull request here: https://github.com/RGLab/flowCore/pull/21 Thanks, Kevin On Thu, Apr 10, 2014 at 3:48 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > My 2ct is that it is worthwhile to have a lean core package. It sounds

Re: [Bioc-devel] Dependency on windowing systems in the flowCore package

2014-04-10 Thread Kasper Daniel Hansen
My 2ct is that it is worthwhile to have a lean core package. It sounds like it would be trivial to separate gating into a new package, and - provided functions are not renamed - would be trivial for downstream packages to adapt to. Especially in situations where competing groups work on the same

Re: [Bioc-devel] Dependency on windowing systems in the flowCore package

2014-04-10 Thread Kevin Ushey
Hi Kieran, Dan, I would suggest that you open an issue at https://github.com/RGLab/flowCore/issues/new. Perhaps the easiest solution is to copy featureSignif from feature into flowCore (giving adequate citation and such, respecting licenses...). It looks like the function doesn't depend too much

Re: [Bioc-devel] seqlevelsStyle<- doesn't work for GRanges object

2014-04-10 Thread Tengfei Yin
forget to say "thank you" in the end :) On Thu, Apr 10, 2014 at 6:22 PM, Tengfei Yin wrote: > Hi all, > > "seqlevelsStyle<-" method does work for me in devel-branch, I haven't dig > into it yet, please check out the code below and its output. > > ## for you to paste > library(GenomicRanges) > gr

[Bioc-devel] seqlevelsStyle<- doesn't work for GRanges object

2014-04-10 Thread Tengfei Yin
Hi all, "seqlevelsStyle<-" method does work for me in devel-branch, I haven't dig into it yet, please check out the code below and its output. ## for you to paste library(GenomicRanges) gr <- GRanges("chr1", IRanges(1, 3)) seqlevelsStyle(gr) ## works seqlevelsStyle(gr) <- "NCBI" ## fail seqnameSt

Re: [Bioc-devel] Dependency on windowing systems in the flowCore package

2014-04-10 Thread Kieran O'Neill
On 10 April 2014 14:26, Dan Tenenbaum wrote: > Hi Kieran, > > > - Original Message - > > From: "Kieran O'Neill" > > To: bioc-devel@r-project.org > > Sent: Thursday, April 10, 2014 2:03:41 PM > > Subject: [Bioc-devel] Dependency on windowing systems in the flowCore > package > > > > In Bi

Re: [Bioc-devel] Dependency on windowing systems in the flowCore package

2014-04-10 Thread Dan Tenenbaum
Hi Kieran, - Original Message - > From: "Kieran O'Neill" > To: bioc-devel@r-project.org > Sent: Thursday, April 10, 2014 2:03:41 PM > Subject: [Bioc-devel] Dependency on windowing systems in the flowCore package > > In Bioconductor, the core infrastructure for loading and representing >

[Bioc-devel] Dependency on windowing systems in the flowCore package

2014-04-10 Thread Kieran O'Neill
In Bioconductor, the core infrastructure for loading and representing flow cytometry data is the flowCore package. It contains some very useful structures, most notably the flowFrame and flowSet classes, as well as read.FCS, which loads the (somewhat complicated, binary) FCS file format. However,

Re: [Bioc-devel] Old version of packages

2014-04-10 Thread Gustavo H. Esteves
Thank you Dan, this really solved my problem. Best regards Gustavo On Thu, Apr 10, 2014 at 12:18 PM, Dan Tenenbaum wrote: > > - Original Message - > > From: "Gustavo H. Esteves" > > To: "BioC Devel - List" > > Sent: Thursday, April 10, 2014 8:08:29 AM > > Subject: [Bioc-devel] Ol

Re: [Bioc-devel] Old version of packages

2014-04-10 Thread Dan Tenenbaum
- Original Message - > From: "Gustavo H. Esteves" > To: "BioC Devel - List" > Sent: Thursday, April 10, 2014 8:08:29 AM > Subject: [Bioc-devel] Old version of packages > > Dear Bioc-devel members > > is it possible to recover an old version of any package from > Bioconductor? Yes, if

[Bioc-devel] metadata() in BiocGenerics?

2014-04-10 Thread Vincent Carey
seems like something we should use more routinely, and it was not straightforward for me to find it in IRanges [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Old version of packages

2014-04-10 Thread Gustavo H. Esteves
Dear Bioc-devel members is it possible to recover an old version of any package from Bioconductor? Thanks -- Gustavo Henrique Esteves [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/ma