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\begin{document}
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\title{Computations related to the Bioinformatics Applications
Note, 2009}
\author{VJ Carey stvjc at channing.harvard.edu}
\maketitle

The main illustrations in the Applications note involve
a gene set.  All chunks have eval=FALSE; to run this code, please
manually reset.

<<geta,eval=FALSE>>=
library(GGtools)
library(GSEABase)
load(system.file("genesets/hla2set.rda", package="GGtools"))
hla2set
@

We need to filter the full HapMap CEU cohort to founders:
<<aasd,eval=FALSE>>=
library(GGdata)
hmceuB36 = getSS("GGdata", as.character(1:22))
hmFou = hmceuB36[, which(hmceuB36$isFounder == TRUE)]
@

Now we run the tests:
<<dorun,eval=FALSE>>=
hla2run = gwSnpTests(hla2set~male, hmFou, snpdepth(250))
@

\end{document}
