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.sqlite", > package="GenomicFeatures") > txdb <- loadDb(samplefile) > ## This works fine > fiveUTRsByTranscript(txdb) > ## This breaks > seqlevels(txdb, force=TRUE) <- "chr6" > fiveUTRsByTranscript(txdb) > Error in relist(x, f) : > shape of 'skeleton' is not compatible with 'NROW(flesh)' > > Deep in the guts of this you are trying to build a GRanges object with > NAs as seqlevels, and it doesn't really like that. > > Florian > > > sessionInfo() > R version 3.0.1 RC (2013-05-12 r62736) > Platform: i386-apple-darwin12.3.0/i386 (32-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel grid stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] GenomicFeatures_1.13.37 AnnotationDbi_1.23.23 Biobase_2.21.7 > [4] GenomicRanges_1.13.43 XVector_0.1.4 IRanges_1.19.36 > [7] BiocGenerics_0.7.5 Gviz_1.5.11 BiocInstaller_1.11.4 > > loaded via a namespace (and not attached): > [1] biomaRt_2.17.2 Biostrings_2.29.18 biovizBase_1.9.2 > [4] bitops_1.0-6 BSgenome_1.29.1 cluster_1.14.4 > [7] colorspace_1.2-2 DBI_0.2-7 dichromat_2.0-0 > [10] Hmisc_3.12-2 labeling_0.2 lattice_0.20-23 > [13] munsell_0.4.2 plyr_1.8 RColorBrewer_1.0-5 > [16] RCurl_1.95-4.1 rpart_4.1-3 Rsamtools_1.13.39 > [19] RSQLite_0.11.4 rtracklayer_1.21.11 scales_0.2.3 > [22] stats4_3.0.1 stringr_0.6.2 tools_3.0.1 > [25] XML_3.98-1.1 zlibbioc_1.7.0 > > > > From: Marc Carlson <mcarl...@fhcrc.org <mailto:mcarl...@fhcrc.org>> > Date: Friday, September 13, 2013 7:38 PM > To: Florian Hahne <florian.ha...@novartis.com > <mailto:florian.ha...@novartis.com>> > Cc: "bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>" > <bioc-devel@r-project.org <mailto:bioc-devel@r-project.org>> > Subject: Re: 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 isActiveSeq was different from seqlevels > was just because it was born for a TranscriptDb (which is based on > an annotation database) instead of being born on a GRanges > object. So seqlevels was the more general tool. > > Marc > > > > On 09/13/2013 07:24 AM, Hahne, Florian wrote: >> 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 help("GenomicFeatures-deprecated"). >> 3: 'isActiveSeq<-' is deprecated. >> Use 'seqlevels' instead. >> See help("Deprecated") and help("GenomicFeatures-deprecated"). >> 4: 'isActiveSeq<-' is deprecated. >> Use 'seqlevels' instead. >> See help("Deprecated") and help("GenomicFeatures-deprecated"). >> 5: 'isActiveSeq' is deprecated. >> Use 'seqlevels' instead. >> See help("Deprecated") and help("GenomicFeatures-deprecated"). >> 6: 'isActiveSeq<-' is deprecated. >> Use 'seqlevels' instead. >> See help("Deprecated") and help("GenomicFeatures-deprecated"). >> >> So has the whole idea of active chromosomes in the data base been >> dropped? I could not find anything in the change notes. Do I get >> it right that you can now do >> seqlevels(txdb, force=TRUE) <- "chr1" >> if you just want the first chromosome to be active? >> >> Florian >> > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel