Differences

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--- mkatari-bioinformatics-august-2013-loadingphytozome [2013/08/21 09:26] – created mkatari
+++ mkatari-bioinformatics-august-2013-loadingphytozome [2015/06/18 08:00] – mkatari
@@ Line 5: / Line 5: @@
 ===== Read Phytozome annotation file. =====
-This step was tricky because there were characters such as quotes and hash marks. We need to reset the default values to allow the file to load without a problem.
+This step was tricky because there were characters such as quotes and hash marks. We need to reset the default values to allow the file to load without a problem. Download the Arabidopsis annotation file here [[https://drive.google.com/file/d/0B172nc4dAaaOUUI1T2ZJamgtdlE/view?usp=sharing|here]]
 <code>
-anno<-read.table("Mesculenta_147_annotation_info.txt",
+anno<-read.table("Athaliana_167_TAIR10.annotation_info.txt",
            header=FALSE,
            sep="\t",
@@ Line 21: / Line 21: @@
 justGeneGo<-anno[,c(2,10)]
 source("createGOdata.R")
+</code>
+===== Run Fisher Exact Test =====
+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<-read.table("resSig.txt", header=T)
+</code>
+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:
+<code>
+source("GoTermEnrichment.R")
+goterm_annot<-read.table("goterm_annot", sep="|", strip.white=TRUE,
+                          row.names=1, quote="")
+goresults=doFisherTest(as.character(gene.list[,1]), goAnnot=goterm_annot)
+write.table(goresults, "goresults.xls", col.names=NA, quote=F, sep="\t")
 </code>