[Bioc-devel] big file ReactomeFI --> bioC annotate package
Valerie.Obenchain at roswellpark.org
Tue Apr 5 17:11:33 CEST 2016
I can help you put together an annotation package.
Here are the general 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 if you have
On 04/05/2016 02:18 AM, Karim Mezhoud wrote:
> Dear bioC developer,
> I included in my bioCancer/inst/extdata a Reactome FI database (/
> 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?
> [[alternative HTML version deleted]]
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