Differences

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--- mkatari-bioinformatics-august-2013-deseq [2013/08/23 16:28] – mkatari
+++ mkatari-bioinformatics-august-2013-deseq [2015/06/17 06:14] – mkatari
@@ Line 9: / Line 9: @@
 source("http://bioconductor.org/biocLite.R")
 biocLite("DESeq")
-</code>
-Once we have installed the DESeq package in our local R repository we need to let our script know to look in this directory so if anyone wants to run our script, it will know exactly where to look for DESeq. R uses a variable (.libPaths) to store locations where it should look for packages. By default R will look in the global R library and the user's local path (if one exists). We will simply add our R library path to this variable. The other option is to tell the system administrator to add the packages to the global library path. This is done in the following lines of the code:
-<code>
-.libPaths(new='/home/mkatari/R/x86_64-unknown-linux-gnu-library/3.0')
 </code>
@@ Line 114: / Line 108: @@
 </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>