Differences

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--- mkatari-bioinformatics-august-2013-deseq [2013/08/23 16:20] – mkatari
+++ mkatari-bioinformatics-august-2013-deseq [2013/08/23 16:26] – mkatari
@@ Line 95: / Line 95: @@
 <code>
-pdf("MAplot.pdf")
+maFile = paste(pathToOutputDir, "MAplot.pdf", sep="")
+pdf(maFile)
 plotMA(res)
 dev.off()
 </code>
-#To get the genes that have FDR of 10%
+#To get the genes that have FDR of 10% and save it in the output directory.
+<code>
+resSig = res[ which(res$padj < 0.1), ]
+outfile = paste(pathToOutputDir,"Deseq.results.txt", sep="")
 write.table(resSig,
-            pathToOutput,
+            outfile,
             sep="\t",
             col.names=T,
             row.names=F,
             quote=F)
+</code>
+Now the beauty of the script is that a user does not need to start R or even know how to use R to run the script. Simply call the script as any command and the results will be saved in an output directory. This is also great way to build a workflow of several R functions. The command to run the script is shown below. Feel free to put it in your sbatch file.
+<code>
+/export/apps/R/3.0.0/bin/Rscript /home/mkatari/Rscripts/DESeq.R /home/mkatari/testDeseq/NextGenRaw.txt /home/mkatari/testDeseq/expdesign.txt /home/mkatari/testDeseq/
+<code>