mkatari-bioinformatics-august-2013-deseq
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
mkatari-bioinformatics-august-2013-deseq [2013/08/23 16:13] – mkatari | mkatari-bioinformatics-august-2013-deseq [2015/06/17 06:14] – mkatari | ||
---|---|---|---|
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:// | ||
Line 95: | Line 88: | ||
< | < | ||
- | 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) | ||
+ | </ | ||
+ | Now the beauty of the script is that a user does not need to start R or even know how to use R to run the script. Simply call the script as any command and the results will be saved in an output directory. This is also great way to build a workflow of several R functions. The command to run the script is shown below. Feel free to put it in your sbatch file. | ||
+ | |||
+ | < | ||
+ | / | ||
+ | </ |
mkatari-bioinformatics-august-2013-deseq.txt · Last modified: 2015/08/21 14:13 by mkatari