[BioC] GenomicFeatures question

[Marc Carlson]

Hi Paul,

Vince is right and those mouse and human specific packages are just
older packages and are only here for legacy support.  Going forward we
aim to make GenomicFeatures more flexible.  To this end we have provided
support to get tracks from UCSC and data from biomaRt and to
automatically assemble a database for you with an organism/build of your
choosing.  Vince is also right that using saveFeatures() and
loadFeatures() is how you should manage the data you download so that
your research will be reproducible.

For a more complete treatment of how to make the most of this package,
please see the latest version of the GenomicFeatures vignette called
"Making and Utilizing TranscriptDb Objects" (which was recently
revamped).  You can find it here:

http://www.bioconductor.org/packages/devel/bioc/html/GenomicFeatures.html

Hope this helps, if you have more questions after seeing the new
vignette let us know so we can improve the documentation,


  Marc


On 03/26/2010 09:50 AM, Vincent Carey wrote:
> The current devel version of GenomicFeatures is 0.4.9
>
> The GenomicFeatures.[org].[inst].[version] packages will, I believe, exist
> only as legacy.
>
> To make comparable resources for local use, use the functions
> makeTranscriptDb* from GenomicFeatures.  These functions generate SQLite
> databases; use saveFeatures and loadFeatures to manage persistent serialized
> versions.
>
> Further clarifications will no doubt come from the developers.
>
> On Thu, Mar 25, 2010 at 8:00 PM, Paul Leo <p.leo at uq.edu.au> wrote:
>
>   
>> First up want a great library, incredibly useful. thanks!
>>
>> But I'm just a little confused by GenomicFeatures.Hsapiens.UCSC.hg18 and
>> GenomicFeatures.Mmusculus.UCSC.mm9 .
>>
>> that is
>> library(GenomicFeatures)
>> library(GenomicFeatures.Mmusculus.UCSC.mm9)
>> library(GenomicFeatures.Hsapiens.UCSC.hg18)
>>
>>
>>     
>>>   txdb <- loadFeatures(system.file("extdata",
>>>       
>> "UCSC_knownGene_sample.sqlite",
>> package="GenomicFeatures",lib.loc="/home/pleo/R_latest/library")) ## NO
>> problem
>>     
>>>   txdb <-
>>>       
>> loadFeatures(system.file("extdata","GenomicFeatures.Mmusculus.UCSC.mm9.sqlite",
>> package="GenomicFeatures.Mmusculus.UCSC.mm9",lib.loc="/home/pleo/R_latest/library")
>> )
>> Error in validObject(.Object) :
>>  invalid class "TranscriptDb" object: the DB has no metadata table
>>     
>>>   txdb <-
>>>       
>> loadFeatures(system.file("extdata","GenomicFeatures.Hsapiens.UCSC.hg18.sqlite",
>> package="GenomicFeatures.Hsapiens.UCSC.hg18",lib.loc="/home/pleo/R_latest/library")
>> )
>> Error in validObject(.Object) :
>>  invalid class
>>
>> Otherwise they usable by the geneHuman() or geneMouse() functions...
>>
>> But I'm not sure what the missing meta table is about: how to the
>> GenomicFeatures.Mmusculus.UCSC.mm9 etc differ from the example
>> GenomicFeaures sql used as GenomicFeature example files (in the first)
>> line
>> Also what is the motivation fro putting them in the Experimental Data
>> section are you thinking these won't be supported/updated  by Biocore
>> Data team in the future?
>>
>> Thanks
>> Paul
>>
>>
>>     
>>> sessionInfo()
>>>       
>> R version 2.11.0 Under development (unstable) (2010-03-23 r51373)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>>  [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
>>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>  [1] GenomicFeatures.Hsapiens.UCSC.hg18_0.1.2
>>  [2] org.Mm.eg.db_2.4.0
>>  [3] RSQLite_0.8-4
>>  [4] DBI_0.2-5
>>  [5] AnnotationDbi_1.9.6
>>  [6] Biobase_2.7.5
>>  [7] GenomicFeatures.Mmusculus.UCSC.mm9_0.1.2
>>  [8] GenomicFeatures_0.4.4
>>  [9] GenomicRanges_0.0.9
>> [10] IRanges_1.5.69
>>
>> loaded via a namespace (and not attached):
>> [1] biomaRt_2.3.4      Biostrings_2.15.25 BSgenome_1.15.16   RCurl_1.3-1
>> [5] rtracklayer_1.7.11 tcltk_2.11.0       tools_2.11.0       XML_2.8-1
>>     
>>>       
>>
>>
>>
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>>
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>>     
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