[BioC] retrieving annotation

Kathi Zarnack zarnack at ebi.ac.uk
Thu Nov 7 14:11:43 CET 2013


I wanted to ask whether any of the annotation packages contains 
information on the transcript biotype (protein-coding, etc). I would 
like to select only protein-coding isoforms from Ensembl annotation, but 
I could not find any package that includes this information (otherwise I 
will get it with biomaRt, I just wondered whether it is already included 

Also, I tried to download GENCODE annotation using GenomicFeatures, and 
got the following error:

 > test=makeTranscriptDbFromUCSC(genome="hg19", 
Error in tableNames(ucscTableQuery(session, track = track)) :
   error in evaluating the argument 'object' in selecting a method for 
function 'tableNames': Error in normArgTrack(track, trackids) : Unknown 
track: Gencode Genes

I tried to get the same table for hg18, but I get only one step further:

Download the wgEncodeGencodeManualV3 table ... OK
Download the wgEncodeGencodeClassesV3 table ... Error in 
normArgTable(value, x) :
   unknown table name 'wgEncodeGencodeClassesV3'

Thank you very much for your help,


 > sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets methods
[8] base

other attached packages:
[1] GenomicFeatures_1.14.0 AnnotationDbi_1.24.0 Biobase_2.22.0
[4] GenomicRanges_1.14.3   XVector_0.2.0 IRanges_1.20.5
[7] BiocGenerics_0.8.0     BiocInstaller_1.12.0

loaded via a namespace (and not attached):
  [1] biomaRt_2.18.0     Biostrings_2.30.0  bitops_1.0-6 BSgenome_1.30.0
  [5] DBI_0.2-7          RCurl_1.95-4.1     Rsamtools_1.14.1 RSQLite_0.11.4
  [9] rtracklayer_1.22.0 stats4_3.0.2       tcltk_3.0.2 tools_3.0.2
[13] XML_3.98-1.1       zlibbioc_1.8.0

Dr. Kathi Zarnack
Luscombe Group

European Molecular Biology Laboratory
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom

emailzarnack at ebi.ac.uk
tel +44 1223 494 526

More information about the Bioconductor mailing list