Re: [Bioc-devel] coercing DataFrame to data.frame

Cool, thanks for the clarification. From: Michael Lawrence mailto:lawrence.mich...@gene.com>> Date: Friday, September 13, 2013 7:24 PM To: Florian Hahne mailto:florian.ha...@novartis.com>> Cc: "bioc-devel@r-project.org" mailto:bioc-devel@r-project.org>> Subject

Re: [Bioc-devel] isActiveSeq deprecated

Makes sense. Thanks. I'll update my code. Florian From: Marc Carlson mailto:mcarl...@fhcrc.org>> Date: Friday, September 13, 2013 7:38 PM To: Florian Hahne mailto:florian.ha...@novartis.com>> Cc: "bioc-devel@r-project.org" mailto:bioc-devel@r-project.org>> Subjec

Re: [Bioc-devel] IRanges: 'extractROWS' fails for 'RangedData'

Hi, It seems the issue has been resolved with the latest bioc build. Best wishes Julian On 09/15/2013 04:01 PM, Julian Gehring wrote: Hi, calling 'head' or 'tail' on a 'RangedData' objects fail with the lastest builds (R: 2013-09-14 r63932, IRanges: 1.19.35). The cause seems to be that ther

Re: [Bioc-devel] [BioC] plot methylation figure for end analysis

I agree that the profile or metagene plot is useful and widely applied. Creating such a plot consists of several steps, including: - quantifying and accumulating signal around sites of interest - normalization - visualization The qProfile() function in QuasR was designed to do the quantification/

Re: [Bioc-devel] isActiveSeq deprecated

Hey Marc, I think your move towards seqlevels is not quite working yet: samplefile <- system.file("extdata", "UCSC_knownGene_sample.sqlite", package="GenomicFeatures") txdb <- loadDb(samplefile) ## This works fine fiveUTRsByTranscript(txdb) ## This breaks seqlevels(txdb, force=TRUE) <- "chr6" fiv

Re: [Bioc-devel] isActiveSeq deprecated

Thanks Florian, I just checked in a fix for this. Please let me know if you find any other quirks. Marc On 09/16/2013 05:33 AM, Hahne, Florian wrote: > Hey Marc, > I think your move towards seqlevels is not quite working yet: > > samplefile <- system.file("extdata", "UCSC_knownGene_sample.

Re: [Bioc-devel] R-version

On 09/15/2013 07:12 AM, Wolfgang Huber wrote: Dear Julian thanks. Since this has come up here and elsewhere, and since the next Bioc release is coming up, let's remind ourselves that we should make development against 3.0.1 Patched (2013-09-03 r63824) -- "Good Sport". Martin - should this be

[Bioc-devel] R and Bioconductor versions for the forthcoming release

Bioconductor developers: The Bioc release schedule is available http://bioconductor.org/developers/release-schedule/ A reminder that version 2.13 of Bioconductor will be released on October 15, and will work with R-3.0.2. Package authors should be testing the Bioc 'devel' version of their p