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mkatari-bioinformatics-august-2013-deseq [2013/08/23 14:18] – created mkatarimkatari-bioinformatics-august-2013-deseq [2013/08/23 14:41] – mkatari
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-[[mkatari-bioinformatics-august-2013|Manny's Bioinformatics Workshop]]+[[mkatari-bioinformatics-august-2013|Back to Manny's Bioinformatics Workshop HOME]]
  
 Here we will discuss how to create an R script that can be executed on HPC. Majority of the script is the same except for the first few commands that read the arguments from command line. Here we will discuss how to create an R script that can be executed on HPC. Majority of the script is the same except for the first few commands that read the arguments from command line.
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 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]] 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]]
  
-#counts = read.table("NextGenRaw.txt", header=T, row.names=1)+You have to first load the file into your workspace. 
 + 
 +If you are running it locally 
 +<code> 
 +counts = read.table("NextGenRaw.txt", header=T, row.names=1) 
 +</code> 
 +If you are writing a script
 counts = read.table(pathToCountsData, header=T, row.names=1) counts = read.table(pathToCountsData, header=T, row.names=1)
  
mkatari-bioinformatics-august-2013-deseq.txt · Last modified: 2015/08/21 14:13 by mkatari