[Genabel-commits] r1119 - in pkg/ProbABEL: doc src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Mar 8 16:33:41 CET 2013
Author: lckarssen
Date: 2013-03-08 16:33:41 +0100 (Fri, 08 Mar 2013)
New Revision: 1119
Modified:
pkg/ProbABEL/doc/ProbABEL_manual.tex
pkg/ProbABEL/src/Makefile.am
Log:
Fix bug #2598 in ProbABEL: The prepare_data.R script is mentioned in the manual, but not distributed in .deb or .tar.gz
Unfortunately the changes in the manual also include a bunch of changes only in the white space as I was in the process of replacing tabs with spaces.
Modified: pkg/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- pkg/ProbABEL/doc/ProbABEL_manual.tex 2013-03-08 14:52:16 UTC (rev 1118)
+++ pkg/ProbABEL/doc/ProbABEL_manual.tex 2013-03-08 15:33:41 UTC (rev 1119)
@@ -293,27 +293,27 @@
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
@@ -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.
@@ -344,7 +344,7 @@
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
@@ -355,7 +355,7 @@
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}
@@ -494,9 +494,10 @@
\section{Preparing input files}
-In the \texttt{bin} directory you can find the
-\texttt{prepare\_data.R} file -- an R script that arranges phenotypic
-data in right format. Please read this script for details.
+After installing \PA{} you can find the \texttt{prepare\_data.R} file
+in the \texttt{scripts} directory. It is an R script that arranges
+phenotypic data in the right format. Please read this script for
+details.
\section{Memory use and performance}
Maximum likelihood regression is implemented in
Modified: pkg/ProbABEL/src/Makefile.am
===================================================================
--- pkg/ProbABEL/src/Makefile.am 2013-03-08 14:52:16 UTC (rev 1118)
+++ pkg/ProbABEL/src/Makefile.am 2013-03-08 15:33:41 UTC (rev 1119)
@@ -6,7 +6,7 @@
REGFILES = data.h data.cpp gendata.h gendata.cpp mematrix.h mematri1.h \
command_line_settings.h command_line_settings.cpp reg1.h usage.h \
usage.cpp main.cpp utilities.h utilities.cpp phedata.h phedata.cpp \
- cholesky.h cholesky.cpp regdata.h regdata.cpp \
+ cholesky.h cholesky.cpp regdata.h regdata.cpp \
maskedmatrix.cpp maskedmatrix.h reg1.cpp
EIGENFILES = eigen_mematrix.h eigen_mematrix.cpp
@@ -70,6 +70,10 @@
## Install these scripts in the bin directory as well:
dist_bin_SCRIPTS = probabel.pl extIDS.pl
+## Install this R script in the examples directory
+scriptdir = $(pkgdatadir)/scripts
+dist_script_DATA = prepare_data.R
+
## Install the config file
dist_sysconf_DATA = probabel_config.cfg.example
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