[BioC] TxDb.Hsapiens.UCSC.hg19.knownGene: seqlevels() vs isActive()

[Marc Carlson]

Hi Andrew,

This post probably belonged on bioc-devel since you are talking only 
about the development branch.

But thanks for mentioning this.  To answer your question: there was not 
in fact any new version of the annotation package.  The code for this is 
actually in GenomicFeatures where I have been deprecating isActiveSeq 
(as it is now largely redundant with seqinfo and the related functions).

Also, I fixed this yesterday.  So pretty soon you should not get any 
more mysterious warnings in devel.


   Marc



On 08/22/2013 10:26 AM, Andrew Jaffe wrote:
> Was there a new version of TxDb.Hsapiens.UCSC.hg19.knownGene in the last
> day or two (v 2.9.2)? It looks like there are some issues with seqlevels
> replacing isActiveSeq() in the new version:
>
>> library(TxDb.Hsapiens.UCSC.hg19.knownGene)
>> txdb=TxDb.Hsapiens.UCSC.hg19.knownGene
> For example, I never call isActiveSeq(), so I'm not sure where the warning
> is coming in:
>
>> seqlevels(txdb,force=TRUE) = paste0("chr",c(1:22,"X","Y","M"))
> Warning message:
> 'isActiveSeq' is deprecated.
> Use 'seqinfo' instead.
> See help("Deprecated") and help("GenomicFeatures-deprecated").
>
> Other calls now throw warning flags for this:
>> introns = intronsByTranscript(txdb)
> Warning messages:
> 1: 'isActiveSeq' is deprecated.
> Use 'seqinfo' instead.
> See help("Deprecated") and help("GenomicFeatures-deprecated").
> 2: 'isActiveSeq' is deprecated.
> Use 'seqinfo' instead.
> See help("Deprecated") and help("GenomicFeatures-deprecated").
> 3: 'isActiveSeq' is deprecated.
> Use 'seqinfo' instead.
> See help("Deprecated") and help("GenomicFeatures-deprecated").
> 4: 'isActiveSeq' is deprecated.
> Use 'seqinfo' instead.
> See help("Deprecated") and help("GenomicFeatures-deprecated").
> 5: 'isActiveSeq' is deprecated.
> Use 'seqinfo' instead.
> See help("Deprecated") and help("GenomicFeatures-deprecated").
> 6: 'isActiveSeq' is deprecated.
> Use 'seqinfo' instead.
> See help("Deprecated") and help("GenomicFeatures-deprecated").
>
> Lastly, some calls work at all, and are met with an error
>
>> utr5 = fiveUTRsByTranscript(txdb)
> Error in validObject(.Object) :
>    invalid class "GRanges" object: 'seqnames' contains missing values
> In addition: Warning messages:
> 1: 'isActiveSeq' is deprecated.
> Use 'seqinfo' instead.
> See help("Deprecated") and help("GenomicFeatures-deprecated").
> 2: 'isActiveSeq' is deprecated.
> Use 'seqinfo' instead.
> See help("Deprecated") and help("GenomicFeatures-deprecated").
> 3: 'isActiveSeq' is deprecated.
> Use 'seqinfo' instead.
> See help("Deprecated") and help("GenomicFeatures-deprecated").
>
> Any help would be appreciated. Below is sessionInfo() results
>
> -Andrew
>
>
>> sessionInfo()
> R Under development (unstable) (2013-08-22 r63646)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>   [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>   [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
>   [7] LC_PAPER=en_US.iso885915       LC_NAME=C
>   [9] LC_ADDRESS=C                   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices datasets  utils     methods
> [8] base
>
> other attached packages:
> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2
> [2] GenomicFeatures_1.13.32
> [3] AnnotationDbi_1.23.18
> [4] Biobase_2.21.6
> [5] GenomicRanges_1.13.36
> [6] XVector_0.1.0
> [7] IRanges_1.19.24
> [8] BiocGenerics_0.7.4
>
> loaded via a namespace (and not attached):
>   [1] biomaRt_2.17.2     Biostrings_2.29.15 bitops_1.0-6
> BSgenome_1.29.1
>   [5] DBI_0.2-7          RCurl_1.95-4.1     Rsamtools_1.13.29  RSQLite_0.11.4
>   [9] rtracklayer_1.21.9 stats4_3.1.0       tools_3.1.0        XML_3.98-1.1
> [13] zlibbioc_1.7.0
>
> 	[[alternative HTML version deleted]]
>
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