[GenABEL-dev] [Genabel-commits] r1839 - pkg/OmicABELnoMM/doc
L.C. Karssen
lennart at karssen.org
Thu Oct 23 11:46:02 CEST 2014
On 23-10-14 11:19, Frank, Alvaro Jesus wrote:
> If you set it up I will for sure use it.
> I have no idea how to.
Sure, no problem!
Lennart.
> ________________________________________
> 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
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>>
>
> --
> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
> GPG key ID: A88F554A
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>
--
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands
lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
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