[GenABEL-dev] [Genabel-commits] r1839 - pkg/OmicABELnoMM/doc

Thu Oct 23 11:19:04 CEST 2014

If you set it up I will for sure use it.
I have no idea how to.
________________________________________
From: genabel-devel-bounces at lists.r-forge.r-project.org [genabel-devel-bounces at lists.r-forge.r-project.org] on behalf of L.C. Karssen [lennart at karssen.org]
Sent: Thursday, October 23, 2014 11:15 AM
To: genabel-devel at lists.r-forge.r-project.org
Subject: Re: [GenABEL-dev] [Genabel-commits] r1839 - pkg/OmicABELnoMM/doc

Hi Alvaro,

On 22-10-14 15:06, noreply at r-forge.r-project.org wrote:
> Author: afrank
> Date: 2014-10-22 15:06:36 +0200 (Wed, 22 Oct 2014)
> New Revision: 1839
>
> Added:
>    pkg/OmicABELnoMM/doc/UserGuide.tex
>    pkg/OmicABELnoMM/doc/userguide.pdf
> Log:
> Added documentation Latex barebone and PDF.

Thanks for starting to work on the documentation, one of the most
valuable parts of a project.

If you haven't already done so it may be good to see how we use
autotools to generate the PDF from LaTeX source in ProbABEL. Don't
hesitate to ask me for help if you have difficulty understanding parts
of it as it is not very trivial. I must admit that it is not 100% fool
proof because we don't test for the existence of all LaTeX packages in
use. But for someone with a proper TeXLive install it should work (and
there is the --disable-latex-doc option for those who have the pdflatex
binary (which autoconf looks for), but miss other packages).

One thing about the PDF: could you please remove it from SVN? Since the
PDF can be generated from the source files it doesn't belong in a
version control system.
Moreover, once creation of the PDF has been automated by autotools a
'make clean' will simply delete it, which may cause confusion when
committing.

Best,

Lennart.

>
> Added: pkg/OmicABELnoMM/doc/UserGuide.tex
> ===================================================================
> --- pkg/OmicABELnoMM/doc/UserGuide.tex                                (rev 0)
> +++ pkg/OmicABELnoMM/doc/UserGuide.tex        2014-10-22 13:06:36 UTC (rev 1839)
> @@ -0,0 +1,173 @@
> +\documentclass{report}
> +
> +\usepackage{fullpage}
> +
> +\usepackage{graphicx,color}
> +\usepackage{mhchem}
> +\usepackage{xcolor}
> +\usepackage{listings}
> +
> +
> +\lstdefinestyle{BASH}
> +{
> +    backgroundcolor=\color{black},
> +    basicstyle=\scriptsize\color{white}\ttfamily
> +}
> +
> +
> +\begin{document}
> +
> +\title{OmicabelNoMM User's Guide}
> +\author{Alvaro Frank}
> +\date{October 2014}
> +\maketitle
> +
> +
> +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> +\chapter{Quick Usage}
> +
> +
> +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> +\chapter{Understanding OmicabelNoMM}
> +
> +\section{Overview}
> +
> +\section{Glossary}
> +
> +\section{Formulas}
> +
> +\subsection{Possible analysis}
> +
> +\subsubsection{Basic analysis}
> +\begin{align}
> +y &\sim \beta_0 1 + \beta_1 x \\
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_r x_r\\
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_{l+1} x_{l+1}  + \dots + \beta_p x_p\\
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_{r} \left(x_{l+1}  + \dots +  x_p\right)
> +\end{align}
> +
> +\subsubsection{Analysis with factors/dosages}
> +\begin{align}
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_r \phi_1 x_r\\
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_{l+1}  \phi_1 x_{l+1}  + \dots + \beta_p  \phi_r x_p\\
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_{r} \left( \phi_1 x_{l+1}  + \dots +   \phi_r x_p\right)
> +\end{align}
> +
> +\subsubsection{Analysis with Interactions/Environmental Effects}
> +\begin{align}
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_r i_1 x_r\\
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_{l+1} i_1 x_r + \dots  + \beta_j j_1 x_r\\
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_{r}  i_1 \left( x_{l+1}  + \dots + x_p\right) \\
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_{l+1}  i_1 \left( x_{l+1}  + \dots + x_p\right) +\dots + \beta_{j}  i_j \left( x_{l+1}  + \dots + x_p\right)
> +\end{align}
> +
> +\subsubsection{Analysis with Interactions/Environmental Effects keeping original variable}
> +\begin{align}
> +y &\sim\beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l +  \beta_{l+1} x_r +  \beta_{l+2} i_1 x_r\\
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_{l+1} x_r + \beta_{l+2} i_1 x_r + \dots  + \beta_j j_1 x_r
> +\end{align}
> +
> +\subsubsection{Analysis with Interactions and factors}
> +\begin{align}
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_r i_1 \phi_1 x_r\\
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_{l+1} i_1 \phi_1 x_r + \dots  + \beta_j j_1 \phi_1 x_r\\
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_{r}  i_1 \left( \phi_{l+1} x_{l+1}  + \dots + \phi_p x_p\right) \\
> +y &\sim  \dots + \beta_l cov_l + \beta_{l+1}  i_1 \left(  \phi_{l+1} x_{l+1}  + \dots +  \phi_{p} x_p\right) +\dots + \beta_{j}  i_j \left( \phi_{l+1} x_{l+1}  + \dots + \phi_{p} x_p\right)
> +\end{align}
> +
> +\subsubsection{Analysis with Interactions and factor keeping original variable}
> +\begin{align}
> +y &\sim\beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l +  \beta_{l+1} \phi_{r} x_r +  \beta_{l+2} i_1 \phi_{r} x_r\\
> +y &\sim \beta_0 1 + \beta_1 cov_1 + \dots + \beta_l cov_l + \beta_{l+1} \phi_{r} x_r + \beta_{l+2} i_1 \phi_{r} x_r + \dots  + \beta_j j_1 \phi_{r} x_r
> +\end{align}
> +
> +
> +\subsection{Regression Coefficients}
> +
> +$\beta=(X^T X)^{-1} X^T y$
> +
> +\subsection{T-statistic}
> +\subsection{P-values}
> +
> +
> +\section{Algorithm}
> +
> +\section{Compromises}
> +
> +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> +\chapter{Setting OmicabelNoMM up}
> +
> +\section{Your Machine}
> +
> +\subsection{Clusters vs personal Computers}
> +
> +\section{Source Files}
> +
> +\begin{lstlisting}[style=BASH,escapechar=\%]
> +
> +user at ubuntu:~$ svn checkout svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/OmicABELnoMM
> +Checked out revision 1838.
> +user at ubuntu:~$ cd OmicABELnoMM/
> +user at ubuntu:~/OmicABELnoMM$
> +$%
> +\end{lstlisting}
> +
> +\section{Compilers}
> +
> +\begin{lstlisting}[style=BASH,escapechar=\%]
> +
> +TODO:Install Compilers cmds
> +$%
> +\end{lstlisting}
> +
> +\section{3rd Party Libraries}
> +
> +\begin{lstlisting}[style=BASH,escapechar=\%]
> +
> +TODO:Install BOOST and BLAS LIBRARIES cmds
> +$%
> +\end{lstlisting}
> +
> +\section{Compiling}
> +
> +For compiling the final executable binary use:
> +\begin{lstlisting}[style=BASH,escapechar=\%]
> +
> +user at ubuntu:~/OmicABELnoMM$ make
> +$%
> +\end{lstlisting}
> +
> +For compiling the test binary use:
> +\begin{lstlisting}[style=BASH,escapechar=\%]
> +
> +user at ubuntu:~/OmicABELnoMM$ make check
> +$%
> +\end{lstlisting}
> +
> +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> +\chapter{Preparing Source Data}
> +
> +\section{Overview}
> +\section{Databel}
> +\section{Covariates}
> +\section{Independent Variables, SNPs,CPG Sites,Measurements used to explain other Measurements}
> +\section{Dependent Variable, Phenotypes,Measurements to be explained}
> +
> +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> +\chapter{Running Analysis}
> +
> +\section{WARNING: Theoretical Caveats}
> +
> +\section{Simple Linear Regression}
> +
> +\section{Cluster usage for Simple Linear Regression}
> +
> +\section{Covariates in Linear Regression}
> +
> +\section{Simple interactions of non linear terms, Enviromental Effects}
> +
> +
> +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> +\chapter{FAQ}
> +
> +\end{document}
>
>
> Property changes on: pkg/OmicABELnoMM/doc/UserGuide.tex
> ___________________________________________________________________
> Added: svn:executable
>    + *
>
> Added: pkg/OmicABELnoMM/doc/userguide.pdf
> ===================================================================
> (Binary files differ)
>
>
> Property changes on: pkg/OmicABELnoMM/doc/userguide.pdf
> ___________________________________________________________________
> Added: svn:executable
>    + *
> Added: svn:mime-type
>    + application/octet-stream
>
> _______________________________________________
> Genabel-commits mailing list
> Genabel-commits at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
>

--
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-