[Genabel-commits] r2005 - tutorials/GenABEL_general

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2015-07-08 22:18:20 +0200 (Wed, 08 Jul 2015)
New Revision: 2005

Modified:
   tutorials/GenABEL_general/GenABEL-tutorial.Rnw
   tutorials/GenABEL_general/intro.Rnw
   tutorials/GenABEL_general/probabel.Rnw
   tutorials/GenABEL_general/strat0.Rnw
   tutorials/GenABEL_general/workgwaaclass.Rnw
Log:
Updates to the GenABEL tutorial:
- Fixed some references to undefined labels
- Updated the copyright year on the title page
- Updated the "outdated" message in Chapter 1: Overview.


Modified: tutorials/GenABEL_general/GenABEL-tutorial.Rnw
===================================================================
--- tutorials/GenABEL_general/GenABEL-tutorial.Rnw	2015-07-08 20:12:45 UTC (rev 2004)
+++ tutorials/GenABEL_general/GenABEL-tutorial.Rnw	2015-07-08 20:18:20 UTC (rev 2005)
@@ -163,8 +163,8 @@
 
 \title{GenABEL tutorial}
 %%\title{Introduction to genome-wide association analysis using R}
-\author{Copyright 2014, the GenABEL project developers \\
-Copyright 2007-2013, Yurii Aulchenko}
+\author{Copyright 2014--2015, the GenABEL project developers \\
+Copyright 2007--2013, Yurii Aulchenko}
 
 \begin{document}
 

Modified: tutorials/GenABEL_general/intro.Rnw
===================================================================
--- tutorials/GenABEL_general/intro.Rnw	2015-07-08 20:12:45 UTC (rev 2004)
+++ tutorials/GenABEL_general/intro.Rnw	2015-07-08 20:18:20 UTC (rev 2005)
@@ -2,8 +2,11 @@
 \label{sec:intro}
 \index{overview}
 
-{\bf This introduction is outdated: now the \GA{} is the project, the
-  suite, and the package, see \url{http://www.genabel.org/developers}}
+\textbf{This introduction is outdated: currently GenABEL refers the
+  project, \texttt{GenABEL} refers to the package and then there is
+  the GenABEL suite which is the set of all packages developed under
+  the umbrella of the GenABEL project. See also the text ``The three
+  layers of GenABEL'' at \url{http://www.genabel.org/developers}}
 
 \GA{} is an R library developed to facilitate Genome-Wide
 Association (GWA) analysis of binary and quantitative traits.

Modified: tutorials/GenABEL_general/probabel.Rnw
===================================================================
--- tutorials/GenABEL_general/probabel.Rnw	2015-07-08 20:12:45 UTC (rev 2004)
+++ tutorials/GenABEL_general/probabel.Rnw	2015-07-08 20:18:20 UTC (rev 2005)
@@ -1,6 +1,6 @@
 \chapter{Imperfect knowledge about genotypes}
-
-This chapter is mostly copy-pasted from the \PA{} manual -- the user is 
+\label{sec:impute}
+This chapter is mostly copy-pasted from the \PA{} manual -- the user is
 encouraged to check it directly for the latest version\footnote{The
   \PA{} manual can be found at \url{http://www.genabel.org/manuals/}.}.
 
@@ -415,7 +415,7 @@
 with 1-2 covariates and overnight for logistic regression or the Cox
 proportional hazards model (figures for a PC bought back in 2007).
 
-Memory may be an issue with \PA{} if you use 
+Memory may be an issue with \PA{} if you use
 MACH text dose/probability files, e.g. for large chromosomes,
 such as chromosome one consumed up to 5 GB of RAM with 6,000 people.
 
@@ -426,7 +426,7 @@
 filevector format (functions: \texttt{mach2databel()} and
 \texttt{impute2databel()}, respectively).
 
-When '--mmscore' option is used, the analysis may take quite some time. 
+When '--mmscore' option is used, the analysis may take quite some time.
 
 \section{Methodology}
 \label{sec:methodology}
@@ -744,7 +744,7 @@
 \end{quote}
 A proper reference may look like
 \begin{quote}
-For the analysis of imputed data, we used the \PA{} 
+For the analysis of imputed data, we used the \PA{}
 from the \texttt{GenABEL} suite of programs (Aulchenko \emph{et al.}, 2010).
 \end{quote}
 
@@ -756,5 +756,3 @@
 makes use of the source code of the \texttt{R} package ''\texttt{survival}''
 as implemented by T. Lumley.
 \end{quote}
-
-

Modified: tutorials/GenABEL_general/strat0.Rnw
===================================================================
--- tutorials/GenABEL_general/strat0.Rnw	2015-07-08 20:12:45 UTC (rev 2004)
+++ tutorials/GenABEL_general/strat0.Rnw	2015-07-08 20:18:20 UTC (rev 2005)
@@ -179,10 +179,16 @@
 section \ref{subsec:inbreeding}. The effects of substructure --
 that is when study sample consist of several genetic populations --
 onto genotypic distribution will be considered in section \ref{subsec:wahlund}.
-Finally, we will generalize the obtained results for the
-case of arbitrary structures and will see what are the effects
-of kinship onto joint distribution of genotypes and phenotypes
-in section \ref{subsec:phenocorr}.
+%%
+%% LCK: Commented the following lines because I can't find the
+%% subsec:phenocorr section. Moreover, this dead link was also present
+%% in an old version (from 2010) of the tutorial that I still had lying
+%% around.
+%% 
+% Finally, we will generalize the obtained results for the
+% case of arbitrary structures and will see what are the effects
+% of kinship onto joint distribution of genotypes and phenotypes
+% in section \ref{subsec:phenocorr}.
 
 \subsection{Hardy-Weinberg equilibrium}
 \label{subsec:HWE}

Modified: tutorials/GenABEL_general/workgwaaclass.Rnw
===================================================================
--- tutorials/GenABEL_general/workgwaaclass.Rnw	2015-07-08 20:12:45 UTC (rev 2004)
+++ tutorials/GenABEL_general/workgwaaclass.Rnw	2015-07-08 20:18:20 UTC (rev 2005)
@@ -101,7 +101,8 @@
 as these are stored in an internal format --
 you need to coerce that to another data type if you
 want to manipulate/analyse these data using
-non-\GA{} functions (see section \ref{subs:gwaa}).
+non-\GA{} functions (see below and, for more technical details,
+appendix~\ref{sec:internals}).
 
 The number of individuals described in an
 object of \texttt{gwaa.data-class} can be