%\VignetteIndexEntry{GGBase overview}
%\VignetteDepends{GGtools}
%\VignetteKeywords{Genetical genomics,SNP,expression}
%\VignettePackage{GGBase}


%
% NOTE -- ONLY EDIT THE .Rnw FILE!!!  The .tex file is
% likely to be overwritten.
%
\documentclass[12pt]{article}

\usepackage{amsmath,pstricks}
\usepackage[authoryear,round]{natbib}
\usepackage{hyperref}


\textwidth=6.2in
\textheight=8.5in
%\parskip=.3cm
\oddsidemargin=.1in
\evensidemargin=.1in
\headheight=-.3in

\newcommand{\scscst}{\scriptscriptstyle}
\newcommand{\scst}{\scriptstyle}


\newcommand{\Rfunction}[1]{{\texttt{#1}}}
\newcommand{\Robject}[1]{{\texttt{#1}}}
\newcommand{\Rpackage}[1]{{\textit{#1}}}
\newcommand{\Rmethod}[1]{{\texttt{#1}}}
\newcommand{\Rfunarg}[1]{{\texttt{#1}}}
\newcommand{\Rclass}[1]{{\textit{#1}}}

\textwidth=6.2in

\bibliographystyle{plainnat} 
 
\begin{document}
%\setkeys{Gin}{width=0.55\textwidth}

\title{GGBase: infrastructure for genetics of gene expression}
\author{VJ Carey}
\maketitle

\section{Introduction}

Data representations for
genetics of gene expression in humans must be
as efficient as possible.  Up to Bioconductor 2.1,
integrative genomics experiments could be represented
by racExSet instances as defined in package GGtools.
Genotypes were represented as integers.

For Bioconductor 2.2, we have access to the snpMatrix
package of D. Clayton, and we have introduced the
smlSet class to represent genetics of gene expression
studies with lists of snp.matrix instances, along with
ordinary representations of expression data.

\section{Primary class structure, and associated methods}

<<lkc>>=
library(GGBase)
getClass("smlSet")
library(GGtools)
showMethods(class="smlSet", where="package:GGBase")
showMethods(class="smlSet",  where="package:GGtools")
@

\section{Example data structure}

<<lkd>>=
data(hmceuB36.2021)
hmceuB36.2021
@

\section{SNP location infrastructure}

see the newSNPloc vignette

\section{Conclusion}

The concepts discussed above define the bulk of the tools
supporting the gwSnpScreen method of GGtools.  Consult the
vignette of GGtools for more information.

\end{document}
