\documentclass[a4paper]{article}
\usepackage{Sweave}

\title{Example analysis}
\author{YuriiA}

\begin{document}
\maketitle

\section{Import data to GenABEL}

Load library

<<>>=
library(GenABEL)
@

Convert TPED files to GA format

<<>>=
convert.snp.tped(tped="../usePrimitive/plink.tped",tfam="../usePrimitive/plink.tfam",out="plink.raw")
@

Load the data into R

<<>>=
dta <- load.gwaa.data(pheno="../usePrimitive/phenotypes.txt",geno="plink.raw")
@

\section{Quality control}

Use following threshold parameters

<<>>=
thMAF <- 0.01
thHWE <- 1e-6
@

for quality control

<<>>=
qc <- check.marker(dta,maf=thMAF,p.lev=thHWE)
@

summary of excluded snps and ids

<<>>=
summary(qc)
@

clean the data

<<>>=
dtaQCed <- dta[qc$idok,qc$snpok]
@

generate per-snp summary

<<>>=
smr <- summary(gtdata(dtaQCed))
smr[1:3,]
@

draw a hystogram of effect alelle frequency

\begin{figure}[t]
\centering
<<fig=true,echo=false>>=
hist(smr$Q.2)
@
\end{figure}

\section{Analysis of association}

What phenotypes are there?

<<>>=
phdata(dtaQCed)[1:3,]
@

Analyse association using the score test

<<>>=
qts <- qtscore(coolTrait ~ sex, data = dtaQCed)
@

Show top results

<<>>=
summary(qts)
@

Display graphics

\begin{figure}[t]
\centering
<<fig=true,echo=false>>=
plot(qts)
abline(h=-log10(5e-8))
@
\end{figure}


\end{document}