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 [2015/06/17 06:14] – 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. | ||
Line 9: | Line 9: | ||
source(" | source(" | ||
biocLite(" | biocLite(" | ||
- | </ | ||
- | |||
- | However to make the script easy to run for anyone on the server, we will tell the R script where exactly to look for DESeq. R uses a variable (.libPaths) to store locations where it should look for packages. We will simply add the path to this variable. This way the person running the script does not need to have DESeq installed in their local R libraries. The other option is to tell the system administrator to add the packages. This is done in the following lines of the code | ||
- | |||
- | < | ||
- | mannyLibPaths = '/ | ||
- | .libPaths(new='/ | ||
</ | </ | ||
Line 24: | Line 17: | ||
</ | </ | ||
- | 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. |
< | < | ||
Line 33: | Line 26: | ||
</ | </ | ||
- | 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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< | < | ||
- | pdf(" | + | maFile = paste(pathToOutputDir, |
+ | pdf(maFile) | ||
plotMA(res) | plotMA(res) | ||
dev.off() | dev.off() | ||
</ | </ | ||
- | #To get the genes that have FDR of 10% | + | #To get the genes that have FDR of 10% and save it in the output directory. |
+ | < | ||
+ | resSig = res[ which(res$padj < 0.1), ] | ||
+ | |||
+ | outfile = paste(pathToOutputDir," | ||
write.table(resSig, | write.table(resSig, | ||
- | | + | |
sep=" | sep=" | ||
col.names=T, | col.names=T, | ||
row.names=F, | row.names=F, | ||
quote=F) | quote=F) | ||
+ | </ | ||
+ | |||
- | #DESeq manual: http:// |
mkatari-bioinformatics-august-2013-deseq.txt · Last modified: 2015/08/21 14:13 by mkatari