[Genabel-commits] r1061 - pkg/ProbABEL/doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Dec 22 14:35:49 CET 2012
Author: lckarssen
Date: 2012-12-22 14:35:49 +0100 (Sat, 22 Dec 2012)
New Revision: 1061
Modified:
pkg/ProbABEL/doc/ProbABEL_manual.tex
pkg/ProbABEL/doc/packaging.txt
Log:
Updated ProbABEL documentation for upcoming release of v0.3.0.
- doc/ProbABEL_manual.tex: Bumped version number and minor other reforamatting
- doc/packaging.txt: added instructions on testing other ./configure options when running 'make distcheck'.
Modified: pkg/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- pkg/ProbABEL/doc/ProbABEL_manual.tex 2012-12-21 19:22:46 UTC (rev 1060)
+++ pkg/ProbABEL/doc/ProbABEL_manual.tex 2012-12-22 13:35:49 UTC (rev 1061)
@@ -1,6 +1,6 @@
\documentclass[12pt,a4paper]{article}
-\title{Manual for ProbABEL v0.2.2}
+\title{Manual for ProbABEL v0.3.0}
\author{
Maksim Struchalin$^{1}$, Lennart Karssen$^{1}$, Yurii Aulchenko$^{2}$ \\
\\
@@ -89,7 +89,7 @@
Currently, \PA{} implements linear, logistic regression,
and Cox proportional hazards models. The corresponding analysis
programs are called \texttt{palinear}, \texttt{palogist},
-and \texttt{pacoxph}\footnote{Please note that in ProbABEL v.0.2.2 the
+and \texttt{pacoxph}\footnote{Please note that in ProbABEL v.0.3.0 the
\texttt{pacoxph} program is not built by default because it is still
too buggy for production use. Instructions on how to compile the
\texttt{pacoxph} module can be found in the \texttt{CHANGES.LOG} file
@@ -274,7 +274,7 @@
To run linear regression, you should use the program called
\texttt{palinear}; for logistic analysis use \texttt{palogist}, and
for the Cox proportional hazards model use
-\texttt{pacoxph}\footnote{Please note that in ProbABEL v.0.2.2 the
+\texttt{pacoxph}\footnote{Please note that in ProbABEL v.0.3.0 the
\texttt{pacoxph} program is not built by default because it is still
too buggy for production use. Instructions on how to compile the
\texttt{pacoxph} module can be found in the \texttt{CHANGES.LOG}
@@ -293,31 +293,31 @@
Usage: /tmp/PAInst/bin/palogist options
Options:
- --pheno : phenotype file name
- --info : information (e.g. MLINFO) file name
- --dose : predictor (e.g. MLDOSE/MLPROB) file name
- --map : [optional] map file name
- --nids : [optional] number of people to analyse
- --chrom : [optional] chromosome (to be passed to output)
- --out : [optional] output file name (default is regression.out.txt)
- --skipd : [optional] how many columns to skip in the predictor
- (dose/prob) file (default 2)
- --ntraits : [optional] how many traits are analysed (default 1)
- --ngpreds : [optional] how many predictor columns per marker
- (default 1 = MLDOSE; else use 2 for MLPROB)
- --separat : [optional] character to separate fields (default is space)
- --score : use score test
- --no-head : do not report header line
- --allcov : report estimates for all covariates (large outputs!)
- --interaction: Which covariate to use for interaction with SNP analysis (default is no interaction, 0)
- --interaction_only: like previous but without covariate acting in interaction with SNP (default is no interaction, 0)
- --mmscore : score test in samples of related individuals. File with inverse of variance-covariance matrix (for palinear) or inverse correlation (for palogist) as input parameter
- --robust : report robust (aka sandwich, aka Hubert-White) standard errors
- --help : print help
+ --pheno : phenotype file name
+ --info : information (e.g. MLINFO) file name
+ --dose : predictor (e.g. MLDOSE/MLPROB) file name
+ --map : [optional] map file name
+ --nids : [optional] number of people to analyse
+ --chrom : [optional] chromosome (to be passed to output)
+ --out : [optional] output file name (default is regression.out.txt)
+ --skipd : [optional] how many columns to skip in the predictor
+ (dose/prob) file (default 2)
+ --ntraits : [optional] how many traits are analysed (default 1)
+ --ngpreds : [optional] how many predictor columns per marker
+ (default 1 = MLDOSE; else use 2 for MLPROB)
+ --separat : [optional] character to separate fields (default is space)
+ --score : use score test
+ --no-head : do not report header line
+ --allcov : report estimates for all covariates (large outputs!)
+ --interaction: Which covariate to use for interaction with SNP analysis (default is no interaction, 0)
+ --interaction_only: like previous but without covariate acting in interaction with SNP (default is no interaction, 0)
+ --mmscore : score test in samples of related individuals. File with inverse of variance-covariance matrix (for palinear) or inverse correlation (for palogist) as input parameter
+ --robust : report robust (aka sandwich, aka Hubert-White) standard errors
+ --help : print help
\end{verbatim}
%% --interaction_only: like previos but without covariate acting in
%% interaction with SNP
-%% (default is no ineraction, 0)
+%% (default is no ineraction, 0)
\subsection{Basic analysis options}
@@ -336,7 +336,7 @@
an analysis of height by running
\begin{verbatim}
user at server:~/ProbABEL/examples/$ ../bin/palinear -p height.txt \
- -d test.mldose -i test.mlinfo
+ -d test.mldose -i test.mlinfo
\end{verbatim}
Output from the analysis will be directed to the
\texttt{regression.out.csv} file.
@@ -344,18 +344,18 @@
The analysis of a binary trait (e.g.~chd) can be run with
\begin{verbatim}
user at server:~/ProbABEL/examples/$ ../bin/palogist -p logist_data.txt \
- -d test.mldose -i test.mlinfo
+ -d test.mldose -i test.mlinfo
\end{verbatim}
To run a Cox proportional hazards model\footnote{Please note that in
- ProbABEL v.0.2.2 the \texttt{pacoxph} program is not built by
+ ProbABEL v.0.3.0 the \texttt{pacoxph} program is not built by
default because it is still too buggy for production
use. Instructions on how to compile the \texttt{pacoxph} module can
be found in the \texttt{CHANGES.LOG} file in the \texttt{doc/}
directory of the installation package.}, try
\begin{verbatim}
user at server:~/ProbABEL/examples/$ ../bin/pacoxph -p coxph_data.txt \
- -d test.mldose -i test.mlinfo
+ -d test.mldose -i test.mlinfo
\end{verbatim}
Please have a look at the shell script files \texttt{example\_qt.sh},
@@ -367,8 +367,8 @@
genetic predictors per SNP, e.g.~you can run linear model with
\begin{verbatim}
user at server:~/ProbABEL/examples/$ ../bin/palinear -p height.txt \
- -d test.mlprob -i test.mlinfo \
- --ngpreds=2
+ -d test.mlprob -i test.mlinfo \
+ --ngpreds=2
\end{verbatim}
\subsection{Advanced analysis options}
@@ -838,7 +838,7 @@
\end{quote}
A proper reference may look like
\begin{quote}
-For the analysis of imputed data, we used the \PA{} v.0.2.2
+For the analysis of imputed data, we used the \PA{} v.0.3.0
from the \texttt{GenABEL} suite of programs (Aulchenko \emph{et al.}, 2010).
\end{quote}
@@ -869,7 +869,7 @@
%\hline
%Distribution & $\mu$ & $\tau^2$ & $v(\mu)$ \\
%\hline
-%Normal & $\eta$ & $\sigma^2$ & \\
+%Normal & $\eta$ & $\sigma^2$ & \\
%Binomial & $1/(1+e^{-\eta})$ & & \\
%Poisson & $e^{\eta}$ & & \\
%\hline
Modified: pkg/ProbABEL/doc/packaging.txt
===================================================================
--- pkg/ProbABEL/doc/packaging.txt 2012-12-21 19:22:46 UTC (rev 1060)
+++ pkg/ProbABEL/doc/packaging.txt 2012-12-22 13:35:49 UTC (rev 1061)
@@ -9,13 +9,22 @@
- fakeroot
- lintian
- devscripts (not necessary, but has some nice utilities like dch)
-** Building the package for the first time
+** Checking whether the source code builds correctly
First check to see if everything compiles and all files are included
- in the automake files:
+ in the automake files (if you have multi-core CPU with e.g. 4
+ cores, you can add the -j4 option to the make commands):
./configure
make distcheck
If there are no errors, a tar.gz file of the source should have been
- created. Let's create the package.
+ created. We will use this file in the next step where the actual
+ package is built. But first we need to check whether the source
+ builds correctly for various settings of the ./configure
+ options. Run the following:
+ DISTCHECK_CONFIGURE_FLAGS="--disable-eigen" make distcheck
+ DISTCHECK_CONFIGURE_FLAGS="--enable-pacoxph" make distcheck
+** Building the package for the first time
+ Now that we verified that the source code builds without problems,
+ let's create the package.
mkdir /tmp/PA-deb
cp ProbABEL-0.2.0.tar.gz /tmp/PA-deb
cd /tmp/PA-deb
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