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 <mcarlson@fhcrc.org <mailto:mcarlson@fhcrc.org>>
> Date: Friday, September 13, 2013 7:38 PM
> To: Florian Hahne <florian.hahne@novartis.com 
> <mailto:florian.hahne@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
>>
>


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