mkatari-bioinformatics-august-2013-deseq
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mkatari-bioinformatics-august-2013-deseq [2013/08/23 14:18] – created mkatari | mkatari-bioinformatics-august-2013-deseq [2013/08/23 15:23] – mkatari | ||
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- | [[mkatari-bioinformatics-august-2013|Manny' | + | [[mkatari-bioinformatics-august-2013|Back to Manny' |
- | Here we will discuss how to create an R script that can be executed on HPC. Majority of the script is the same except | + | Here we will discuss how to create an R 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. | ||
- | In order to install DESeq type the following: | + | In order to install DESeq type the following: |
< | < | ||
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</ | </ | ||
- | However | + | However |
< | < | ||
Line 24: | Line 24: | ||
</ | </ | ||
- | Now for our script we will use a command | + | Now for our script we will use a function (commandArgs) |
< | < | ||
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</ | </ | ||
+ | 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. | ||
The input for DESeq is a matrix/ | The input for DESeq is a matrix/ | ||
- | #counts = read.table(" | + | You have to first load the file into your workspace. |
+ | |||
+ | If you are running it locally | ||
+ | < | ||
+ | counts = read.table(" | ||
+ | </ | ||
+ | If you are writing a script | ||
+ | < | ||
counts = read.table(pathToCountsData, | counts = read.table(pathToCountsData, | ||
+ | </ | ||
#This is simply meta-data to store information about the samples. | #This is simply meta-data to store information about the samples. |
mkatari-bioinformatics-august-2013-deseq.txt · Last modified: 2015/08/21 14:13 by mkatari