Hi, Can we pass our own ontology in function hyperGTest ? Muhammad Javed, Ph.D. Software Developer/Research Associate Advaita Corporation www.AdvaitaBio.com

Hi Muhammad, Probably the closest we have come (so far) towards supporting this is described here: http://www.bioconductor.org/packages/release/bioc/vignettes/GOstats/in st/doc/GOstatsForUnsupportedOrganisms.pdf You can see with the KEGG example how a very flat set of annotations can be tested, and with GO how a real DAG can be tested. So by extending the relevant classes I think you probably could do that without too much trouble. Marc On 03/17/2014 08:49 AM, Muhammad Javed wrote: > Hi, > > Can we pass our own ontology in function hyperGTest ? > > > Muhammad Javed, Ph.D. > Software Developer/Research Associate > Advaita Corporation > www.AdvaitaBio.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor