[Bioc-devel] big file ReactomeFI --> bioC annotate package

[Obenchain, Valerie]

There are helper functions in GenomicFeatures to make TxDbs from various
types of data:

library(GenomicFeatures)

> makeTxDb <hit tab>
makeTxDb                    makeTxDbFromGFF            
makeTxDbFromUCSC            makeTxDbPackageFromBiomart 
makeTxDbFromBiomart         makeTxDbFromGRanges        
makeTxDbPackage             makeTxDbPackageFromUCSC

Also see section 4 of the package vignette 'Creating New TxDb Objects or
Packages':

browseVignettes("GenomicFeatures")

and the man page ?makeTxDb.


Valerie



On 04/06/2016 07:16 AM, Karim Mezhoud wrote:
> Thank you Valerie,
> TxDb uses sqlite format. Maybe I need to know how to convert
> reactomeFI.txt to reactomeFI.sqlite.
>
> I found from    bioC workshop 2006 a  Lab: How to use SQLite
> <http://master.bioconductor.org/help/course-materials/2006/rforbioinformatics/labs/thurs/SQLite-R-howto.pdf>  
> .
> Is it a good starting tutorial?
> Any tutorial is welcome.
> Thanks
> Karim
>
>
>
>
> On Tue, Apr 5, 2016 at 4:11 PM, Obenchain, Valerie
> <Valerie.Obenchain at roswellpark.org
> <mailto:Valerie.Obenchain at roswellpark.org>> wrote:
>
>     Hi Karim,
>
>     I can help you put together an annotation package.
>
>     Here are the general guidelines:
>
>     http://www.bioconductor.org/developers/package-guidelines/
>
>     We ask that annotations packages implement the select() interface from
>     AnnotationDbi (eg, keys(), columns(), keytypes(), etc.). You can
>     see how
>     select() works with the TxDb and OrgDb packages. Once you've got that
>     working you can open a new ticket on the package tracker.
>
>     Feel free to write me at valerie.obenchain at roswellpark.org
>     <mailto:valerie.obenchain at roswellpark.org> if you have
>     other questions.
>
>     Valerie
>
>
>
>
>     On 04/05/2016 02:18 AM, Karim Mezhoud wrote:
>     > Dear bioC developer,
>     > I included in my bioCancer/inst/extdata a Reactome FI database (/
>     >
>     http://reactomews.oicr.on.ca:8080/caBigR3WebApp2015/FIsInGene_031516_with_annotations.txt.zip
>     > )
>     >
>     > Gene1    Gene2    Annotation    Direction    Score
>     > 16-5-5    CDC42    predicted    -    0.82
>     > 16-5-5    RHOJ    predicted    -    0.82
>     > 16-5-5    RHOQ    predicted    -    0.82
>     > <DELTA>FAS/APO-1/CD95    BID    activate    ->    1.00
>     > <DELTA>FAS/APO-1/CD95    CASP10    complex    -    1.00
>     > <DELTA>FAS/APO-1/CD95    DAXX    complex; reaction    -    1.00
>     > <DELTA>FAS/APO-1/CD95    DKFZP686N0154    activate    ->    1.00
>     > <DELTA>FAS/APO-1/CD95    FADD    complex    -    1.00
>     > <DELTA>FAS/APO-1/CD95    FASLG    complex; input    -    1.00
>     > <DELTA>FAS/APO-1/CD95    HSPB1    reaction    -    1.00
>     > <DELTA>FAS/APO-1/CD95    MAP2K3    activate    ->    1.00
>     > <DELTA>FAS/APO-1/CD95    MAP2K4    activate    ->    1.00
>     >
>     > bioCancer uses this file to extract the Direction/arrowhead of
>     gene-gene
>     > interaction (activates, inhibits, predicted, complexe.....).
>     > This kind of data is not available in Reactome.db package nor by
>     Reactome
>     > API service (to my knowledge).
>     >
>     > I have to remove this file from my new package and may get
>     annotate package
>     > for ReactomeFI database.
>     > How to?
>     > Karim
>     >
>     >       [[alternative HTML version deleted]]
>     >
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