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+%\VignetteIndexEntry{crlmm Vignette - Genotyping}

+%\VignetteDepends{crlmm, hapmapsnp6, genomewidesnp6Crlmm}

+%\VignetteKeywords{genotype, crlmm, SNP 5, SNP 6}

+%\VignettePackage{crlmm}

+\documentclass{article}

+

+\newcommand{\Rfunction}[1]{{\texttt{#1}}}

+\newcommand{\Rmethod}[1]{{\texttt{#1}}}

+\newcommand{\Rcode}[1]{{\texttt{#1}}}

+\newcommand{\Robject}[1]{{\texttt{#1}}}

+\newcommand{\Rpackage}[1]{{\textsf{#1}}}

+\newcommand{\Rclass}[1]{{\textit{#1}}}

+\newcommand{\oligo}{\Rpackage{oligo }}

+

+\begin{document}

+\title{Genotyping with the \Rpackage{crlmm} Package}

+\date{March, 2009}

+\author{Benilton Carvalho}

+\maketitle

+

+<<setup, echo=FALSE, results=hide>>=

+options(width=60)

+options(continue=" ")

+options(prompt="R> ")

+@ 

+

+\section{Quick intro to \Rpackage{crlmm}}

+

+The \Rpackage{crlmm} package contains a new implementation for the

+CRLMM algorithm (Carvalho et. al. 2007). Our focus is on efficient

+genotyping of SNP 5.0 and 6.0 Affymetrix arrays, although extensions

+of the method are under development for similar platforms.

+

+This implementation, compared to the previous one (in

+\Rpackage{oligo}), offers improved confidence scores, quality scores

+for SNP's and batches, higher accuracy on different datasets and

+better performance.

+

+Additionally, this package does not use the pd.genomewidesnp packages

+created via pdInfoBuilder for \Rpackage{oligo}. Instead, it uses

+different annotation packages (\Rpackage{genomewidesnp.5} and

+\Rpackage{genomewidesnp.6}), which use simple R objects to store only

+the information needed for genotyping. This allowed us to improve the

+speed of the method, as SQL queries are no longer performed here.

+

+It is also our priority to make the package simple to use. Below we

+demonstrate how to get genotype calls with the 'new' CRLMM. We use 3

+samples on SNP 5.0 made available via the \Rpackage{hapmapsnp5}

+package.

+

+<<crlmm>>=

+require(oligoClasses)

+library(crlmm)

+library(hapmapsnp6)

+path <- system.file("celFiles", package="hapmapsnp6")

+celFiles <- list.celfiles(path, full.names=TRUE)

+system.time(crlmmResult <- crlmm(celFiles, verbose=FALSE))

+@ 

+

+The \Robject{crlmmResult} is a \Rclass{SnpSet} (see Biobase) object.

+\begin{itemize}

+\item \Robject{calls}: genotype calls (1 - AA; 2 - AB; 3 - BB);

+\item \Robject{confs}: confidence scores, which can be translated to probabilities by using:

+  \[ 1-2^-(\mbox{confs}/1000), \] although we prefer this

+  representation as it saves a significant amount of memory;

+\item \Robject{SNPQC}: SNP quality score;

+%%\item \Robject{batchQC}: Batch quality score;

+\item \Robject{SNR}: Signal-to-noise ratio.

+\end{itemize}

+

+<<out>>=

+calls(crlmmResult)[1:10,]

+confs(crlmmResult)[1:10,]

+crlmmResult[["SNR"]]

+@ 

+

+\section{Details}

+

+This document was written using:

+

+<<>>=

+sessionInfo()

+@ 

+

+

+\end{document}