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--- mkatari-bioinformatics-august-2013-loadingphytozome [2013/08/21 09:26] – created mkatari
+++ mkatari-bioinformatics-august-2013-loadingphytozome [2014/05/08 12:10] – mkatari
@@ Line 21: / Line 21: @@
 justGeneGo<-anno[,c(2,10)]
 source("createGOdata.R")
+</code>
+===== Run Fisher Exact Test =====
+ 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>
+Start by sourcing the [[https://drive.google.com/file/d/0B172nc4dAaaObThyRjlZT0xjRE0/edit?usp=sharing|GoTermEnrichment.R]] script. The function itself is called doFisherTest. It has four arguments: gene.list, gene2go , go2gene, and goAnnot. The first is your list of genes. The next two use gene2go and go2gene as default but different lists can be provided here and the Last is an annotation file for the terms. Download goterm_annot [[https://docs.google.com/a/nyu.edu/file/d/0B172nc4dAaaOWFVWdDdpcmxjamc/edit|here]]
+To run the function:
+<code>
+source("GoTermEnrichment.R")
+goterm_annot<-read.table("goterm_annot", sep="|", strip.white=TRUE,
+                          row.names=1, quote="")
+goresults=doFisherTest(gene.list, goAnnot=goterm_annot)
+write.table(goresults, "goresults", quote=F, sep="\t")
 </code>