[Bioc-devel] isActiveSeq deprecated

Hi Marc, I saw these warnings in Gviz, but they stem from GenomicFeatures Warning messages: 1: 'isActiveSeq' is deprecated. Use 'seqlevels' instead. See help("Deprecated") and help("GenomicFeatures-deprecated"). 2: 'isActiveSeq' is deprecated. Use 'seqlevels' instead. See help("Deprecated") and he

Re: [Bioc-devel] isActiveSeq deprecated

Hi Florian, Yes we are trying to make things more uniform. seqlevels() lets you rename as well as deactivate chromosomes you want to ignore, so it was really redundant with isActiveSeq(). So we are moving away from isActiveSeq() just so that users have less to learn about. The reason why is

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] 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] isActiveSeq deprecated

Hi Marc, Wouldn't it make sense to just ignore the 'force' arg when dropping the seqlevels of a TranscriptDb? The 'force' argument is FALSE by default and this prevents seqlevels<- to shrink GRanges or other vector-like objects when the user tries to drop seqlevels that are in use. Internally se

Re: [Bioc-devel] isActiveSeq deprecated

I actually considered this, but I opted to do it this way just for the sake of being consistent (which was my whole mission for implementing seqlevels in here in the 1st place). Now I could make it more convenient here and break consistency with how it is used elsewhere, but what do people pre

Re: [Bioc-devel] isActiveSeq deprecated

Note that currently it's kind of inconsistent anyway because it doesn't look at the seqlevels that are in use. For example: library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene Trying to drop chrUn_gl000249 (which I know is not in use): > seqlevels(txdb) <-

Re: [Bioc-devel] isActiveSeq deprecated

Hi Marc, Herve, I also noticed this behaviour: library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene seqlevels(txdb, force=TRUE) <- c("chr1", "ch2") oldLevs <- seqlevels(txdb) seqlevels(txdb, force=TRUE) <- "chr1" seqlevels(txdb, force=TRUE) <- oldLevs Error in .seq

Re: [Bioc-devel] isActiveSeq deprecated

Hi Florian, Marc, On 09/18/2013 11:55 PM, Hahne, Florian wrote: Hi Marc, Herve, I also noticed this behaviour: library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene seqlevels(txdb, force=TRUE) <- c("chr1", "ch2") oldLevs <- seqlevels(txdb) seqlevels(txdb, force=TR

Re: [Bioc-devel] isActiveSeq deprecated

Same view here, with all the different data types that are around in the Bioconductor world these days it seems to me that a consistent behaviour is preferable. Florian On 9/24/13 8:22 AM, "Hervé Pagès" wrote: >Hi Florian, Marc, > >On 09/18/2013 11:55 PM, Hahne, Florian wrote: >> Hi Marc, Herve

Re: [Bioc-devel] isActiveSeq deprecated

Thanks for your feedback Florian. We're in the process of revisiting the mechanism for selecting chromosomes on a TranscriptDb object. Expect an update on this soon. H. On 10/01/2013 12:18 AM, Hahne, Florian wrote: Same view here, with all the different data types that are around in the Biocon