[Genabel-commits] r1981 - branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc

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

Author: lckarssen
Date: 2015-05-23 23:47:56 +0200 (Sat, 23 May 2015)
New Revision: 1981

Modified:
   branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc/ProbABEL_manual.tex
Log:
Summary: Minor Updates to the ProbABEL documentation

- Corrected some \mathbf{'some Greek letter'} to \boldsymbol{'some Greek letter'}.
- Changed name of YuriiA Consulting to the new name PolyOmica.
- Updated ProbABEL version number from 0.4.4 to 0.4.5.
- Updated Eigen version number to the current one.


Modified: branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc/ProbABEL_manual.tex	2015-05-19 14:31:01 UTC (rev 1980)
+++ branches/ProbABEL-v0.4.4-hotfix/ProbABEL/doc/ProbABEL_manual.tex	2015-05-23 21:47:56 UTC (rev 1981)
@@ -1,17 +1,17 @@
 \documentclass[12pt,a4paper]{article}
 
-\title{Manual for ProbABEL v0.4.4}
+\title{Manual for ProbABEL v0.4.5}
 \author{\emph{Current Programmers:} Lennart Karssen$^{1,2}$, Maarten
   Kooyman$^2$, \\
   Yurii Aulchenko$^{1,3}$ \\
   \emph{Former Programmers:} Maksim Struchalin
   \\
   \\
-  $^{1}${\small YuriiA Consulting} \\
-  $^{2}${\small Erasmus MC, Rotterdam}\\
+  $^{1}${\small PolyOmica, Groningen, The Netherlands} \\
+  $^{2}${\small Erasmus MC, Rotterdam, The Netherlands}\\
   $^{3}${\small Institute of Cytology and Genetics SD RAS, Novosibirsk}
 }
-\date{November 7, 2014}
+\date{May 24, 2015}
 
 
 \usepackage[utf8]{inputenc}
@@ -223,22 +223,22 @@
 it will speed up your analyses considerably. Moreover, we plan to
 remove the non-EIGEN part of the code in a future release. So, go to
 \url{http://eigen.tuxfamily.org} and download the \texttt{tar.gz} file
-of the latest version of EIGEN (3.2.1 at the time of writing). Extract
+of the latest version of EIGEN (3.2.4 at the time of writing). Extract
 the files:
 \begin{lstlisting}
-user at server:~$ tar -xzf 3.2.1.tar.gz
+user at server:~$ tar -xzf 3.2.4.tar.gz
 \end{lstlisting}
 This will create a directory called \texttt{eigen-eigen} followed by a
 series of letters and digits. For simplicity we rename it to EIGEN
 \begin{lstlisting}
-user at server:~$ mv eigen-eigen-6b38706d90a9 EIGEN
+user at server:~$ mv eigen-eigen-10219c95fe65 EIGEN
 \end{lstlisting}
 
 Now it's time to extract the \PA{} source code and move into the
 directory that is created:
 \begin{lstlisting}
-user at server:~$ tar -xzf probabel-0.4.4.tar.gz
-user at server:~$ cd probabel-0.4.4
+user at server:~$ tar -xzf probabel-0.4.5.tar.gz
+user at server:~$ cd probabel-0.4.5
 \end{lstlisting}
 With the following command we will indicate where the EIGEN files can
 be found and where we want to install \PA{}. Let's install in a
@@ -464,7 +464,7 @@
 short explanation to the command line options:
 \begin{verbatim}
 user at server:~$ palogist --help
-probabel v. 0.4.4
+probabel v. 0.4.5
 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR
 
 Using EIGEN version 3.1.2 for matrix operations
@@ -878,20 +878,20 @@
 Abecasis (2007). The general analysis model is a linear mixed model
 where the expectation of the trait is defined as
 $$
-E[\mathbf{Y}] = \mathbf{X} \mathbf{\beta},
+E[\mathbf{Y}] = \mathbf{X} \boldsymbol{\beta},
 $$
 identical to that defined for a linear model
 (cf.~Eq.~\ref{eq:expectation}). To account for correlations between
 the phenotypes of relatives which may be induced by family relations
 the variance-covariance matrix is defined to be proportional to the
 linear combination of the identity matrix $\mathbf{I}$ and the
-relationship matrix $\mathbf{\Phi}$:
+relationship matrix $\boldsymbol{\Phi}$:
 $$
-\mathbf{V}_{\sigma^2,h^2} = \sigma^2 \left( 2 h^2 \mathbf{\Phi} + (1-h^2)
+\mathbf{V}_{\sigma^2,h^2} = \sigma^2 \left( 2 h^2 \boldsymbol{\Phi} + (1-h^2)
 \mathbf{I} \right),
 $$
 where $h^2$ is the heritability of the trait. The relationship matrix
-$\mathbf{\Phi}$ is twice the matrix containing the coefficients of
+$\boldsymbol{\Phi}$ is twice the matrix containing the coefficients of
 kinship between all pairs of individuals under consideration; its
 estimation is discussed separately in section \ref{kinship}.
 
@@ -910,19 +910,19 @@
 models fit in GWAS (e.g.\ effects of sex, age, etc.), and the part
 including SNP information, $\mathbf{X_g}$:
 $$
-E[\mathbf{Y}] = \mathbf{X}_x \mathbf{\beta}_x +
-\mathbf{X}_g \mathbf{\beta}_g.
+E[\mathbf{Y}] = \mathbf{X}_x \boldsymbol{\beta}_x +
+\mathbf{X}_g \boldsymbol{\beta}_g.
 $$
 Note that the latter design matrix may include not only the main SNP
 effect, but e.g.\ SNP by environment interaction terms.
 
 In the first step, a linear mixed model not including SNP effects
 $$
-E[\mathbf{Y}] = \mathbf{X}_x \mathbf{\beta}_x
+E[\mathbf{Y}] = \mathbf{X}_x \boldsymbol{\beta}_x
 $$
 is fitted. The maximum likelihood estimates (MLEs) of the model
 parameters (regression coefficients for the fixed effects
-$\hat{\mathbf{\beta}}_x$, the residual variance $\hat{\sigma}^2_x$ and
+$\hat{\boldsymbol{\beta}}_x$, the residual variance $\hat{\sigma}^2_x$ and
 the heritability $\hat{h}^2_x$) can be obtained by numerical
 maximization of the likelihood function
 $$
@@ -978,7 +978,7 @@
 \subsubsection{Estimation of the kinship matrix}
 \label{kinship}
 
-The relationship matrix $\mathbf{\Phi}$ used in estimation of the
+The relationship matrix $\boldsymbol{\Phi}$ used in estimation of the
 linear mixed model for pedigree data is twice the matrix containing
 the coefficients of kinship between all pairs of individuals under consideration.
 This coefficient is defined as the probability that two gametes randomly sampled
@@ -1029,7 +1029,7 @@
 \end{quote}
 A proper reference may look like
 \begin{quote}
-For the analysis of imputed data, we used \PA{} v.0.4.4
+For the analysis of imputed data, we used \PA{} v.0.4.5
 from the \texttt{GenABEL} suite of programs (Aulchenko \emph{et al.}, 2010).
 \end{quote}
 
@@ -1074,3 +1074,8 @@
 \printindex
 
 \end{document}
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End: