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