These are a few simple scripts for an analysis we're doing using the Mouse Diversity Array.

More information about the array can be found at http://cgd.jax.org/tools/diversityarray.shtml

The MouseDivGeno R package for genotyping can be found at http://cgd.jax.org/tools/mousedivgeno/

You will also need to browse to: http://cgd.jax.org/datasets/popgen/diversityarray/yang2011.shtml
From there, you can download the SNPs for your strains of interest (in the
examples below it our download is res591576617.csv)

Quickstart:
    $ curl -O http://cgd.jax.org/tools/mousedivgeno/MouseDivGeno_1.0.3.tar.gz
    $ curl -O http://cgd.jax.org/tools/mousedivgeno/MouseDivData.RData
    $ R CMD INSTALL MouseDivGeno_1.0.3.tar.gz
    $ R
    R> source("http://bioconductor.org/biocLite.R")
    R> biocLite("org.Mm.eg.db")

    $ mkdir celfiles
    $ cp /path/to/cel/files/*.CEL celfiles/

    $ ./get_genotypes.R celfiles genotypes.txt 0.1
      ## takes approx 1.5 hours on a 2.6Ghz MacBook Pro

    $ ./makeplots.sh genotypes.txt res591576617.csv
      ## ~3 minutes with 4 arrays