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\title{GGBase: infrastructure for genetics of gene expression}
\maketitle
\tableofcontents

\section{Introduction}

The GGBase package defines infrastructure for analysis of data
on the genetics of gene expression.  This document is primarily
of concern to developers; for information on conducting analyses
in genetics of expression, please see the vignette for the GGtools package.

\section{Primary class structure, and associated methods}

\texttt{smlSet} is used to denote ``SNP matrix list'' integrative
container for expression plus genotype data.  The \texttt{SnpMatrix}
class is defined in Clayton's \textit{snpStats} package.
<<lkc>>=
library(GGBase)
getClass("smlSet")
showMethods(class="smlSet", where="package:GGBase")
@
Genotype data are stored in a list in the \texttt{smlEnv} environment
to diminish copying as functions are called on the \texttt{smlSet} instance.

\section{Example data structure}

Expression data were published by the Wellcome Trust GENEVAR project
in 2007.  Genotype data are from HapMap phase II.
<<lkd>>=
if ("GGtools" %in% installed.packages()[,1]) {
 library(GGtools)
 s20 = getSS("GGtools", "20")
 s20
}
@

\section{Visualizing a specific gene-SNP relationship}

The SNP rs6060535 was reported as an eQTL for
CPNE1 by Cheung et al in a Nature paper of 2005.
<<lkf,fig=TRUE>>=
if (exists("s20")) {
 plot_EvG(genesym("CPNE1"), rsid("rs6060535"), s20)
} else plot(1) # pdf must exist....
@

\section{Genotype representations}

The \texttt{SnpMatrix} class of the \textit{snpStats} package
is used to represent genotypes.  Imputed genotypes and their uncertainties
can be represented in this scheme, but the example does not depict this.

<<lkgt,keep.source=TRUE>>=
if (exists("s20")) {
# raw bytes
 as(smList(s20)[[1]], "matrix")[1:5,1:5]
# generic calls
 as(smList(s20)[[1]], "character")[1:5,1:5]
# risk allele (alphabetically later nucleotide) counts
 as(smList(s20)[[1]], "numeric")[1:5,1:5]
}
@

\section{Reducing memory footprint of integrative data structures}

When millions of genotypes are recorded, it can be cumbersome to
work with all simultaneously in memory, and it is seldom scientifically
relevant to do so.  Thus a packaging protocol has been established
in conjunction with the \texttt{getSS} function to allow chromosome-at-a-time
loading of genotype data in conjunction with expression data.

To deploy the packaging protocol, use the \texttt{externalize} function on
a ``one-time'' full smlSet representation of the data, or mimic the behavior
of this function by creating a new package folder structure and populating the
inst/parts with rda files representing a partition (usually by chromosome)
of the genotype SnpMatrix instances.

\end{document}
