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--- mkatari-bioinformatics-august-2013-deseq [2013/08/23 15:23] – mkatari
+++ mkatari-bioinformatics-august-2013-deseq [2013/08/23 15:46] – mkatari
@@ Line 24: / Line 24: @@
 </code>
-Now for our script we will use a function (commandArgs) that allows the R to read in arguments from command line automatically. We will use a command Rscript to run one of our R scripts (DESeq.R). This will be helpful when we are using an R script in an analysis pipeline. The code that reads arguments from the command line are:
+Now in our script we will use a function (commandArgs) that will allow us to read in arguments from command line automatically. We will use the command Rscript followed by our code (DESeq.R) and the arguments will follow. The code will read one word at a time and save it as a character vector:
 <code>
@@ Line 33: / Line 33: @@
 </code>
-All the arguments provided in command line will be saved as a character vector in userargs. The value TRUE in the commandArgs argument make sure only the trailing arguments are saved (which is what we will be providing. If the value is FALSE you will see additional R arguments when the command Rscript is executed.
+This will save all the words as a character vector in userargs. The value TRUE in the commandArgs argument make sure only the trailing arguments are saved. If the value is FALSE you will see additional R arguments when the command Rscript is executed. Notice the order of arguments is important. First we will provide the path to the count data file, then the path to the file containing the experimental design and finally the path to the directory where to save the results.
-The input for DESeq is a matrix/data.frame containing read counts. An example is provided [[https://docs.google.com/file/d/0B172nc4dAaaOMG44Zk1BT2NFdkU/edit?usp=sharing|here]]
+An example of the count data file is provided [[https://docs.google.com/file/d/0B172nc4dAaaOMG44Zk1BT2NFdkU/edit?usp=sharing|here]]
-You have to first load the file into your workspace.
+First we will load the count data file.
-If you are running it locally
-<code>
-counts = read.table("NextGenRaw.txt", header=T, row.names=1)
-</code>
-If you are writing a script
 <code>
 counts = read.table(pathToCountsData, header=T, row.names=1)