Monday, September 14, 2009

Find the function you're looking for in R

Any R user no matter what level of experience has had trouble finding the package or the function to do what you want to do and then figuring out how to use it.  The sos package in R just made that a lot easier.

First, fire up R, then install the sos package (don't omit the quotes):


It'll ask you to choose a mirror.  Choose the closest one.  After it installs, load the package (omit the quotes this time):


This loaded all the functions that come with the sos package, including a particularly useful one called findFn.  It scans the "function" entries in Jonathan Baron's "R site search" database.  Give it a try, using "epistasis" with the quotes as the keyword.


This should open up a web browser that displays relevant functions, the package you need to download (using the above procedure) to use the function, and a link to the help page for that function.

You can also use ??? as an alias for findFn.  Try it like this (use the quotes):

???"genome wide"

Once you have the sos package installed, type vignette("sos") for more information on how to use various functions in this package.

If you still can't find what you're looking for, check out my previous post on finding help on R, and if all else fails, don't forget about Theresa Scott's free weekly R clinic / Q&A sessions.

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Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License.