[Bioc-sig-seq] GenomicFeatures, biomart support

[Hervé Pagès]

Hi,

GenomicFeatures 0.4.5 (in devel) now supports the following databases
in addition to ensembl: bacterial_mart_4, fungal_mart_4, metazoa_mart_4,
plant_mart_4, protist_mart_4 and Ensembl56.

Note that only ensembl and Ensembl56 have CDS information.
For example, for Arabidopsis, you'll get a warning that the
CDS information is missing:

   > txdb <- makeTranscriptDbFromBiomart("plant_mart_4", 
"athaliana_eg_gene")
   Warning message:
   In .normargSplicings(splicings, unique_tx_ids) :
     no CDS information for this TranscriptDb object
   > txdb
   TranscriptDb object:
   | Db type: TranscriptDb
   | Data source: BioMart
   | BioMart database: plant_mart_4
   | BioMart dataset: athaliana_eg_gene
   | BioMart dataset description: Arabidopsis thaliana genes (TAIR9)
   | BioMart dataset version: TAIR9
   | Full dataset: yes
   | transcript_nrow: 39640
   | exon_nrow: 176581
   | cds_nrow: 0
   | Db created by: GenomicFeatures package from Bioconductor
   | Creation time: 2010-03-22 23:32:17 -0700 (Mon, 22 Mar 2010)
   | GenomicFeatures version at creation time: 0.4.5
   | RSQLite version at creation time: 0.8-4

Thanks for your feedback. Let us know if you find any other problem with
the GenomicFeaturess package.

Cheers,
H.


pterry at huskers.unl.edu wrote:
>  Dear bioc-sig-sequencing,
> 
> I would like to annotate chip-seq peaks for the arabidopsis genome.  I note that the GenomicFeatures vignette, section 2.7.3 of the pdf file "Making & using TranscriptDb objects", is suggested for Chip-seq experiments.
> 
> Trying the example in section 2.7.3 of the vignette (but substituting arabidopsis for mouse) resulted in an message that only the 'ensembl' database is now supported.
> 
> In what follows, have I selected the appropriate biomart database and dataset for my purpose?  If so, when might GenomicFeatures support them?  If support will not be soon, can someone suggest an alternative approach for my task?
> 
>> mart4_at_eg_gene <-
> +    makeTranscriptDbFromBiomart(biomart = "plant_mart_4",
> +                                dataset = "athaliana_eg_gene")
> Error in makeTranscriptDbFromBiomart(biomart = "plant_mart_4", dataset = "athaliana_eg_gene") :
>   only 'biomart="ensembl"' is supported for now
> 
>> sessionInfo()
> R version 2.11.0 Under development (unstable) (2010-03-18 r51318)
> x86_64-unknown-linux-gnu
> 
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] biomaRt_2.3.4         GenomicFeatures_0.4.2 BSgenome_1.15.15
> [4] Biostrings_2.15.24    GenomicRanges_0.0.4   IRanges_1.5.63
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.7.5      DBI_0.2-5          RCurl_1.3-1        RSQLite_0.8-4
> [5] rtracklayer_1.7.11 tools_2.11.0       XML_2.6-0
> 
> 
> Thanks,
> P. Terry
> pterry at huskers.unl.edu
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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