Thursday, December 15, 2011

Query a MySQL Database from R using RMySQL

I use this all the time, and the setup is dead simple. Follow the code below to load the RMySQL package, connect to a database (here the UCSC genome browser's public MySQL instance), set up a function to make querying easier, and query the database to return results as a data frame.

4 comments:

  1. Hello Stephen, I´d like to talk to you about how you installed RMySQL, I´m a windows user and this packege is not compiled for windows yet. Could you help me please? My name is George.

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  2. George, see if this helps. If not, I'll see if I can get Will (a Windoze guy) to post about how to do this. You'll have to use the RODBC package, and set up a connection to your database server through My Computer --> Administrative Tools --> Data Sources. But it's been way too long since I've done this, and I don't have a PC to test it out on or give you any screenshots. RMySQL is definitely easier and more "portable" if you can get it to work.

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  3. Hello Stephen!
    Can I ask you a question?
    When you do a query to a database, like you did above, is it possible to pass the data directly to a vector?
    I wanna use the data and create a plot/graphic.

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  4. Try something like:

    query("SELECT * FROM table;")$yourvariable

    or


    query("SELECT * FROM table;")[[1]]

    ReplyDelete

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