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--- mkatari-bioinformatics-august-2013-loadingphytozome [2015/06/18 06:24] – mkatari
+++ mkatari-bioinformatics-august-2013-loadingphytozome [2015/06/18 08:00] – mkatari
@@ Line 25: / Line 25: @@
 ===== Run Fisher Exact Test =====
- If you do not have a sample gene list to work with, simply create a random one.
+Let's use the significant genes identified from Deseq as our example. [[https://drive.google.com/file/d/0B172nc4dAaaOM2hvSlZWNG10UW8/view?usp=sharing|resSig]]
 <code>
-gene.list<-names(gene2go)[sample(1:length(names(gene2go)), 500)]
+gene.list<-read.table("resSig.txt", header=T)
 </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  [[https://docs.google.com/a/nyu.edu/file/d/0B172nc4dAaaOWFVWdDdpcmxjamc/edit|goterm_annot]]
+Start by sourcing the [[https://drive.google.com/file/d/0B172nc4dAaaObThyRjlZT0xjRE0/view?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  [[https://docs.google.com/a/nyu.edu/file/d/0B172nc4dAaaOWFVWdDdpcmxjamc/edit|goterm_annot]]
 To run the function:
@@ Line 38: / Line 40: @@
 goterm_annot<-read.table("goterm_annot", sep="|", strip.white=TRUE,
                           row.names=1, quote="")
-goresults=doFisherTest(gene.list, goAnnot=goterm_annot)
+goresults=doFisherTest(as.character(gene.list[,1]), goAnnot=goterm_annot)
-write.table(goresults, "goresults", quote=F, sep="\t")
+write.table(goresults, "goresults.xls", col.names=NA, quote=F, sep="\t")
 </code>