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.obench...@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.obench...@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]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel