mkatari-bioinformatics-august-2013-deseq
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mkatari-bioinformatics-august-2013-deseq [2013/08/23 15:53] – mkatari | mkatari-bioinformatics-august-2013-deseq [2013/08/23 16:20] – mkatari | ||
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[[mkatari-bioinformatics-august-2013|Back to Manny' | [[mkatari-bioinformatics-august-2013|Back to Manny' | ||
- | Here we will discuss how to create an R script (DESeq.R) that can be executed on HPC. Majority of the script | + | Here we will discuss how to create an R script (DESeq.R) that can be executed on HPC. This script |
If you are going to run DESeq in R on your desktop you will have to make sure DESeq is already installed. | If you are going to run DESeq in R on your desktop you will have to make sure DESeq is already installed. | ||
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</ | </ | ||
- | However to make the script | + | Once we have installed |
< | < | ||
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</ | </ | ||
- | Now in our script we will use a function (commandArgs) that will allow us to read in arguments from command line automatically. | + | Now in our script we will use a function (commandArgs) that will allow us to read in arguments from command line automatically. |
< | < | ||
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- | This will save all the words as a character vector | + | Here we are saving |
An example of the count data file is provided [[https:// | An example of the count data file is provided [[https:// | ||
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quote=F) | quote=F) | ||
- | #DESeq manual: http:// |
mkatari-bioinformatics-august-2013-deseq.txt · Last modified: 2015/08/21 14:13 by mkatari