[adegenet-commits] r891 - pkg/inst/doc

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon May 30 19:07:41 CEST 2011 

Author: jombart
Date: 2011-05-30 19:07:41 +0200 (Mon, 30 May 2011)
New Revision: 891

Added:
   pkg/inst/doc/adegenet-genomics.pdf
   pkg/inst/doc/adegenet-genomics.tex
Modified:
   pkg/inst/doc/adegenet-genomics.Rnw
Log:
Intro of the new vignette 'genomics'.


Modified: pkg/inst/doc/adegenet-genomics.Rnw
===================================================================
--- pkg/inst/doc/adegenet-genomics.Rnw	2011-05-30 16:13:54 UTC (rev 890)
+++ pkg/inst/doc/adegenet-genomics.Rnw	2011-05-30 17:07:41 UTC (rev 891)
@@ -1,6 +1,6 @@
 \documentclass{article}
 % \VignettePackage{adegenet-genomics}
-% \VignetteIndexEntry{An introduction to Discriminant Analysis of Principal Components (DAPC)}
+% \VignetteIndexEntry{Analysing genomic data using adegenet}
 
 \usepackage{graphicx}
 \usepackage[colorlinks=true,urlcolor=blue]{hyperref}
@@ -22,8 +22,10 @@
 
 \begin{document}
 
+\SweaveOpts{prefix.string = figs/genomics, echo=TRUE, eval=TRUE, fig = FALSE, eps = FALSE, pdf = TRUE}
 
 
+
 \definecolor{Soutput}{rgb}{0,0,0.56}
 \definecolor{Sinput}{rgb}{0.56,0,0}
 \DefineVerbatimEnvironment{Sinput}{Verbatim}
@@ -36,16 +38,28 @@
 \maketitle
 \tableofcontents
 
+
+
 %%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%
 \section{Introduction}
 %%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%
+Modern sequencing technologies now make complete genomes more widely accessible.
+The subsequent amounts of genetic data pose challenges in terms of storing and handling the data,
+making former tools developed for classical genetic markers such as microsatellite impracticable on
+standard computers.
+Adegenet has developed new object classes dedicated to handling genome-wide polymorphism (SNPs) with
+minimum rapid access memory (RAM) requirements.
 
+Two new formal classes have been implemented: \texttt{SNPbin}, used to store genome-wide SNPs for
+one individual, and \texttt{genlight}, which stored the same information for multiple individuals.
+In this vignette, we present these classes and show how they can be used for genetic data analysis.
 
 
 
 
+
 %%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%
 \section{Classes of objects}
@@ -62,83 +76,43 @@
 %%%%%%%%%%%%%%%%
 
 
-%%%%%%%%%%%%%%%%
-\subsection{Accessors}
-%%%%%%%%%%%%%%%%
 
 
 
-
-
-
-
-
 %%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%
-\section{Describing clusters using \code{dapc}}
+\section{In practice}
 %%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%
 
-
-
 %%%%%%%%%%%%%%%%
-\subsection{Rationale}
+\subsection{Using accessors}
 %%%%%%%%%%%%%%%%
 
 
-%%%%%%%%%%%%%%%%
-\subsection{In practice}
-%%%%%%%%%%%%%%%%
 
-
-
-
-
-
-
-
 %%%%%%%%%%%%%%%%
+\subsection{Data conversions}
 %%%%%%%%%%%%%%%%
-\section{Customizing graphics}
-%%%%%%%%%%%%%%%%
-%%%%%%%%%%%%%%%%
 
 
-%%%%%%%%%%%%%%%%
-\subsection{DAPC scatterplots}
-%%%%%%%%%%%%%%%%
 
 
-
 %%%%%%%%%%%%%%%%
-\subsection{Group memberships}
+\subsection{Principal Component Analysis (PCA)}
 %%%%%%%%%%%%%%%%
 
 
 
-
-
 %%%%%%%%%%%%%%%%
+\subsection{Discriminant Analysis of Principal Components (DAPC)}
 %%%%%%%%%%%%%%%%
-\section{Using supplementary individuals}
-%%%%%%%%%%%%%%%%
-%%%%%%%%%%%%%%%%
 
 
 
-%%%%%%%%%%%%%%%%
-\subsection{Rationale}
-%%%%%%%%%%%%%%%%
 
 
-%%%%%%%%%%%%%%%%
-\subsection{Predicting group membership}
-%%%%%%%%%%%%%%%%
 
 
-%%%%%%%%%%%%%%%%
-\subsection{Representing supplementary individuals}
-%%%%%%%%%%%%%%%%
 
-
 \end{document}

Added: pkg/inst/doc/adegenet-genomics.pdf
===================================================================
--- pkg/inst/doc/adegenet-genomics.pdf	                        (rev 0)
+++ pkg/inst/doc/adegenet-genomics.pdf	2011-05-30 17:07:41 UTC (rev 891)
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+
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 891

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