Hi, I have some candidate CNVs (with chromosomal start and end position known) but these are not in the gene regions but located upstream or downstream of some genes. Is there any tool or R package where I can use CNV information (as input) and use some options that will allow me to conduct the GO analysis for genes located some bps upstream or downstream of the CNVs? You help will be greatly appreciated. Regards, Yadav Sapkota Uni of Alberta [[alternative HTML version deleted]]

Yadav, You might want to try getEnrichedGO function in ChIPpeakAnno package. Best regards, Julie On 5/9/12 3:31 PM, "Yadav Sapkota" <ysapkota at="" ualberta.ca=""> wrote: > Hi, > > I have some candidate CNVs (with chromosomal start and end position known) > but these are not in the gene regions but located upstream or downstream of > some genes. > > Is there any tool or R package where I can use CNV information (as input) > and use some options that will allow me to conduct the GO analysis for > genes located some bps upstream or downstream of the CNVs? > > You help will be greatly appreciated. > > Regards, > Yadav Sapkota > Uni of Alberta > > [[alternative HTML version deleted]] > > _______________________________________________ > 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