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--- mkatari-bioinformatics-august-2013-loadingphytozome [2013/08/21 09:26] – created mkatari
+++ mkatari-bioinformatics-august-2013-loadingphytozome [2013/08/21 09:34] – mkatari
@@ Line 21: / Line 21: @@
 justGeneGo<-anno[,c(2,10)]
 source("createGOdata.R")
+</code>
+===== Run Fisher Exact Test =====
+Start by sourcing the [[https://docs.google.com/file/d/0B172nc4dAaaOcklUNkpFLWJtbmc/edit?usp=sharing|GOTermEnrichment.R]] script. If you do not have a sample gene list to work with, simply create a random one.
+<code>
+gene.list<-names(gene2go)[sample(1:length(names(gene2go)), 500)]
+</code>
+The function itself is called doFisherTest. It has three arguments: gene.list, gene2go , and go2gene. The last two use gene2go and go2gene as default but different lists can be provided here.
+To run the function:
+<code>
+goresults=doFisherTest(gene.list)
 </code>