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--- mkatari-bioinformatics-august-2013-loadingphytozome [2015/06/18 07:24] – mkatari
+++ mkatari-bioinformatics-august-2013-loadingphytozome [2026/07/14 06:11] (current) – external edit 127.0.0.1
@@ Line 29: / Line 29: @@
 <code>
-gene.list<-read.table("resSig.txt")
+gene.list<-read.table("resSig.txt", header=T)
 </code>
@@ Line 41: / Line 41: @@
                           row.names=1, quote="")
 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>
+Visualizing your results in the GO-term graph. Use the RamiGO package. Simply provide the GO terms that are enriched and the corresponding p-value for the go-terms. By default it will save a file to your working directory called RamiGO.png
+<code>
+source("http://bioconductor.org/biocLite.R")
+biocLite("RamiGO")
+library(RamiGO)
+getAmigoTree(rownames(gotermresults)[1:3], c("blue","red","green"),
+             gotermresults$AdjPval[1:3])
+</code>