User Tools

Site Tools


mkatari-bioinformatics-august-2013-loadingphytozome

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision
Previous revision
mkatari-bioinformatics-august-2013-loadingphytozome [2015/06/18 06:27] mkatarimkatari-bioinformatics-august-2013-loadingphytozome [2015/06/18 09:05] (current) – [Run Fisher Exact Test] mkatari
Line 25: Line 25:
 ===== Run Fisher Exact Test ===== ===== 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> <code>
-gene.list<-names(gene2go)[sample(1:length(names(gene2go))500)]+ 
 +gene.list<-read.table("resSig.txt"header=T) 
 </code> </code>
  
Line 38: Line 40:
 goterm_annot<-read.table("goterm_annot", sep="|", strip.white=TRUE,  goterm_annot<-read.table("goterm_annot", sep="|", strip.white=TRUE, 
                           row.names=1, quote="")                           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> </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>
 +
mkatari-bioinformatics-august-2013-loadingphytozome.1434608829.txt.gz · Last modified: 2015/06/18 06:27 by mkatari