[Genabel-commits] r986 - branches/ProbABEL-refactoring/ProbABEL/doc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Oct 24 12:18:55 CEST 2012
Author: lckarssen
Date: 2012-10-24 12:18:55 +0200 (Wed, 24 Oct 2012)
New Revision: 986
Modified:
branches/ProbABEL-refactoring/ProbABEL/doc/CHANGES.LOG
branches/ProbABEL-refactoring/ProbABEL/doc/INSTALL
branches/ProbABEL-refactoring/ProbABEL/doc/ProbABEL_manual.tex
branches/ProbABEL-refactoring/ProbABEL/doc/packaging.txt
branches/ProbABEL-refactoring/ProbABEL/doc/palinear.1
branches/ProbABEL-refactoring/ProbABEL/doc/palogist.1
Log:
Updated the documentation in the ProbABEL-refactoring branch with the docs in trunk. This one was easy as the docs in the branch had not changed since the branch was started.
Modified: branches/ProbABEL-refactoring/ProbABEL/doc/CHANGES.LOG
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/doc/CHANGES.LOG 2012-10-24 10:15:58 UTC (rev 985)
+++ branches/ProbABEL-refactoring/ProbABEL/doc/CHANGES.LOG 2012-10-24 10:18:55 UTC (rev 986)
@@ -1,22 +1,44 @@
-***** v.0.2-0 (2012.03.04)
+*****
+* Fixed bug #2295: the inverse variance-covariance matrix (used with the
+ --mmscore option) was incorrectly subsetted when NAs are present for
+ one or more SNP dosages. As a result the invvarmatrix that was
+ actually used in the regression contained rows and columns of
+ zeroes. Thanks to Maarten Kooyman for reporting this bug.
-* pacoxph will not be built by default, because it is quite buggy. See
- ./configure notes below on how to enable building it anyway.
+* Fixed bug #1186: When .map file is missing (but --map option was
+ given), the wrong error message was displayed. Thanks to Nicola
+ Pirastu for reporting this bug.
+* Fixed bug #2147: The value of the Rsq column in the info file should
+ be > 0, unlike what was mentioned in the documentation.
+* Update of the probabel.pl script and probabel_config.cfg.
+ The .cfg file now accepts the chr separator in multiple locations in the path
+ (thanks to Marijn Verkerk).
+ probabel.pl can now also run Y chromosome analysis and the help
+ message has been updated.
+
+
+***** v.0.2.0 (2012.06.10)
+* The v.0.1-9e fix for working with prob files in pacoxph has been
+ forward-ported to this branch as well (Lennart and Yurii).
+
+* pacoxph will not be built by default, because it is quite buggy. See
+ ./configure notes below on how to enable building it anyway (Lennart).
+
* ProbABEL can now (experimentally!) analyze binary traits accounting
-for relationship structure (thanks to Yurii and Nicola Pirastu). This
-adds '--mmscore' option for logistic regression. Important: compared
-to 'palinear' the matrix which should be supplied to palogist with
---mmscore should contain an inverse of the correlation matrix (not the
-inverse of var-cov matrix, as is the case for 'palinear' with
---mmscore). This matrix can be obtained through (GenABEL notation):
+ for relationship structure (thanks to Yurii and Nicola Pirastu). This
+ adds '--mmscore' option for logistic regression. Important: compared
+ to 'palinear' the matrix which should be supplied to palogist with
+ --mmscore should contain an inverse of the correlation matrix (not the
+ inverse of var-cov matrix, as is the case for 'palinear' with
+ --mmscore). This matrix can be obtained through (GenABEL notation):
h2.object$InvSigma * h2.object$h2an$estimate[length(h2.object$h2an$estimate)]
-where h2.object is the object returned by 'polygenic()'. Documentation
-explains this procedure in more details; a wrapper function to prepare
-and export correct objects for ProbABEL is planned. (thanks to Yurii)
+ where h2.object is the object returned by 'polygenic()'. Documentation
+ explains this procedure in more details; a wrapper function to prepare
+ and export correct objects for ProbABEL is planned. (thanks to Yurii)
* Small changes (thanks to Lennart).
- in probabel.pl the location for the probabel config file is now set
@@ -27,6 +49,7 @@
- The PDF of the LaTeX documentation is now only generated if the
pdflatex binary can be found. So now we also build the documentation
using autotools.
+- On 32bit Linux systems ProbABEL can now also use large (>4GB) input files.
* ProbABEL uses autoconf and automake now (thanks to Lennart).
@@ -44,45 +67,13 @@
This will install the binaries (palinear etc.) in /usr/local/bin/,
the documentation in /usr/local/share/doc/probabel/, the
- probabel_config.cfg file in /usr/local/etc/, and the examples in
+ probabel_config.cfg.example file in /usr/local/etc/, and the examples in
/usr/local/share/ProbABEL/examples/. The ./configure script tests
for the presence of the pdflatex program. If it is not present the
PDF version of the documentation will not be built.
- NOTE: make install will OVERWRITE any file with the same name if it
- already exists. Also the probabel_config.cfg file in
- /usr/local/etc, even if the user modified it with his/her own
- settings. This is one reason why using the package manager for your
- distribution (apt for Debian, yum for RHEL, CentOS, etc., pkgtools
- for Slackware) is recommended. Package managers do note that a file
- has user-made changes and ask what to do (or make a backup).
+ For more information see the file doc/INSTALL.
- To see options, run
-
-./configure --help
-
- The most notable option is
-./configure --prefix=/some/subdirectory
- to install ProbABEL in that subdirectory. Instead of using
- /usr/local/ as install root, it installs in /some/subdirectory.
-
- The second important option is
-./configure --enable-pacoxph
- this enables the building of the pacoxph binary.
-
- To generate a .tar.gz package for distribution run:
-./configure
-make dist
-
- To test if all your changes to the source files will be packaged
- into the tar.gz file correctly run
-./configure
-make distcheck
-
- To clean up all files generated by ./configure and make, run
-make distclean
-
-
In the ProbABEL autotools integration branch:
- Removed the old Makefile
- Added configure.ac that servers as input for auto(re)conf
Modified: branches/ProbABEL-refactoring/ProbABEL/doc/INSTALL
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/doc/INSTALL 2012-10-24 10:15:58 UTC (rev 985)
+++ branches/ProbABEL-refactoring/ProbABEL/doc/INSTALL 2012-10-24 10:18:55 UTC (rev 986)
@@ -12,6 +12,7 @@
following commands:
./configure
make
+make check
make install
This will install the binaries (palinear etc.) in /usr/local/bin/,
@@ -22,12 +23,9 @@
PDF version of the documentation will not be built.
NOTE: make install will OVERWRITE any file with the same name if it
- already exists. Also the probabel_config.cfg file in
- /usr/local/etc, even if the user modified it with his/her own
- settings. This is one reason why using the package manager for your
- distribution (apt for Debian, yum for RHEL, CentOS, etc., pkgtools
- for Slackware) is recommended. Package managers do note that a file
- has user-made changes and ask what to do (or make a backup).
+ already exists. By default the name of the probabel.pl config file is
+ probabel_config.cfg.example. For probabel.pl to work please rename
+ this file to probabel_config.cfg.
To see options, run
@@ -39,6 +37,11 @@
to install ProbABEL in that subdirectory. Instead of using
/usr/local/ as install root directory, it installs in /some/subdirectory.
+ The pacoxph binary will not be built by default because it is too
+ buggy at present. If you want to build and install it anyway use the
+ --enable function of ./configure:
+./configure --enable-pacoxph
+
To generate a .tar.gz package for distribution run:
./configure
make dist
@@ -56,6 +59,9 @@
will uninstall the files previously installed by 'make install'.
+* Making packages for Linux distributions
+ Instructions for creating a package for your favourite Linux
+ distribution can be found in doc/packaging.txt
* Cross-compiling for Windows on Linux
@@ -64,11 +70,15 @@
First, install the necessary MINGW32 packages. On Debian/Ubuntu this
can be done in the following way:
apt-get install mingw32{-binutils,-runtime} gcc-mingw32
+ For 64 bit windows install these packages:
+apt-get install binutils-mingw-w64-i686 gcc-mingw-w64-base gcc-mingw-w64-i686 \
+ mingw-w64-dev g++-mingw-w64 binutils-mingw-w64-x86-64 g++-mingw-w64-i686 \
+ g++-mingw-w64-x86-64 gcc-mingw-w64-x86-64
Now the binaries can be compiled (I've added a prefix so that when
running 'make install' the whole directory structure can be zipped
easily):
-./configure --host=i586-mingw32msvc --build=i686-linux-gnu \
+./configure --host=i686-w64-mingw32 --build=i686-linux-gnu \
--prefix=/tmp/PA --sysconfdir=/tmp/PA/ \
--datarootdir=/tmp/PA --docdir=/tmp/PA/doc
@@ -79,14 +89,15 @@
this example I was using a 32bit Ubuntu install. For a 64 bit linux
system this will be x86_64-linux-gnu. Note that the values for both
these options can be derived from the names of the compiler
- executables, e.g. the gcc-mingw32 Debian package installs the
- folowing C++ compiler: /usr/bin/i586-mingw32msvc-c++.
+ executables, e.g. the gcc-mingw-w64 Debian package installs the
+ following C++ compilers: /usr/bin/i686-w64-mingw32-c++ and
+ /usr/bin/x86_64-w64-mingw32-c++.
The --[somedir] options are used to make the directory structure as
flat as possible so that we don't bother Windows users with
subdirectories like 'share/' and 'etc/'.
Now you can run
-make
+make CFLAGS+="-O3 -static-libgcc -static-libstdc++" CXXFLAGS+="-O3 -static-libgcc -static-libstdc++"
make install
This creates the binaries pacoxph.exe, palinear.exe and
Modified: branches/ProbABEL-refactoring/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/doc/ProbABEL_manual.tex 2012-10-24 10:15:58 UTC (rev 985)
+++ branches/ProbABEL-refactoring/ProbABEL/doc/ProbABEL_manual.tex 2012-10-24 10:18:55 UTC (rev 986)
@@ -1,4 +1,4 @@
-\title{ProbABEL manual}
+\title{Manual for ProbABEL v0.2.0}
\author{
Maksim Struchalin$^{1}$, Lennart Karssen$^{1}$, Yurii Aulchenko$^{1,2}$ \\
\\
@@ -31,9 +31,9 @@
\makeindex
-\newcommand{\PA}{\texttt{ProbABEL-package}}
-\newcommand{\GA}{\texttt{GenABEL-package}}
-\newcommand{\DA}{\texttt{DatABEL-package}}
+\newcommand{\PA}{\texttt{ProbABEL}}
+\newcommand{\GA}{\texttt{GenABEL}}
+\newcommand{\DA}{\texttt{DatABEL}}
\begin{document}
\maketitle
@@ -88,7 +88,11 @@
Currently, \PA{} implements linear, logistic regression,
and Cox proportional hazards models. The corresponding analysis
programs are called \texttt{palinear}, \texttt{palogist},
-and \texttt{pacoxph}.
+and \texttt{pacoxph}\footnote{Please note that in ProbABEL v.0.2.0 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.}.
\section{Input files}
@@ -116,12 +120,13 @@
metrics (``Quality'', the average maximum posterior probability and
``Rsq'', the proportion of variance decrease after imputations).
-Actually,
-for \PA{}, it does not matter what is written in this file --
-this information is just brought forward to the output. However,
-\textbf{it is critical} that the number of columns is seven and the number
-of lines in the file is equal to the number of SNPs in the
-corresponding DOSE file (plus one for the header line).
+Actually, for \PA{}, it (almost) does not matter what is written in
+this file -- this information is simply copied to the output. However,
+\textbf{it is critical} that the number of columns is seven and the
+number of lines in the file is equal to the number of SNPs in the
+corresponding DOSE file (plus one for the header line). Also make sure
+that the ``Rsq'' column contains values $>0$, otherwise you will end
+up with $\beta$'s set to \texttt{nan}.
The example of SNP information file content follows here (also
to be found in \texttt{ProbABEL/examples/test.mlinfo})
@@ -261,8 +266,13 @@
\label{sec:runanalysis}
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} (all are
-found in the \texttt{bin/} directory after you have compiled
+for the Cox proportional hazards model use
+\texttt{pacoxph}\footnote{Please note that in ProbABEL v.0.2.0 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.}
+(all are found in the \texttt{bin/} directory after you have compiled
the program).
There are in total 11 command line options you can specify to the
@@ -272,7 +282,7 @@
line options:
\begin{verbatim}
user at server:~$ palogist
-ProbABEL v. 0.2.0-beta (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR
+ProbABEL v. 0.2.0 (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR
Usage: /tmp/PAInst/bin/palogist options
Options:
@@ -309,11 +319,11 @@
These options are
\texttt{--dose} (or \texttt{-d}),
-specifying the genomic predictor/MLDOSE file described in sub-section \ref{ssec:dosein};
+specifying the genomic predictor/MLDOSE file described in section \ref{ssec:dosein};
\texttt{--pheno} (or \texttt{-p}),
-specifying the phenotypic data file described in sub-section \ref{ssec:phenoin}; and
+specifying the phenotypic data file described in section \ref{ssec:phenoin}; and
\texttt{--info} (or \texttt{-i}),
-specifying the SNP information file described in sub-section \ref{ssec:infoin}.
+specifying the SNP information file described in section \ref{ssec:infoin}.
If you change to the \texttt{examples} directory you can run
an analysis of height by running
@@ -330,7 +340,12 @@
-d test.mldose -i test.mlinfo
\end{verbatim}
-To run a Cox proportional hazards model, try
+To run a Cox proportional hazards model\footnote{Please note that in
+ ProbABEL v.0.2.0 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
@@ -366,16 +381,27 @@
With the option \texttt{--mmscore} a score test for association
between a trait and genetic polymorphisms in samples of related
-individuals is performed. A file with the inverse of the
-variance-covarince matrix goes as input parameter with that option,
-e.g.~\texttt{--mmscore <filename>}. The file has to contain the first
-column with id names exactly like in phenotype file, BUT OMITTING
-people with no measured phenotype. The rest is a matrix. The phenotype
-file in case of using the \texttt{--mmscore} argument may contain any
-amount of covariates (this is different from previous versions). The
-first column contains id names, the second the trait. The others are
-covariates.
+individuals is performed. For quantitative traits (\texttt{palinear})
+a file with the inverse of the variance-covariance matrix goes as input
+parameter with that option, e.g.~\texttt{--mmscore <filename>}. The
+file has to contain the first column with id names exactly like in
+phenotype file, BUT OMITTING people with no measured phenotype. The
+rest is a matrix. The phenotype file in case of using the
+\texttt{--mmscore} argument may contain any amount of covariates (this
+is different from previous versions). The first column contains id
+names, the second the trait. The others are covariates.
+For binary traits (\texttt{palogist}) the file should contain the
+inverse of the correlation matrix. \textbf{Note: this is an
+ experimental feature!} This matrix can be obtained through (in
+GenABEL notation):
+\begin{verbatim}
+ h2.obj$InvSigma * h2.obj$h2an$estimate[length(h2.obj$h2an$estimate)]
+\end{verbatim}
+where \texttt{h2.obj} is the object returned by GenABEL's
+\texttt{polygenic()}. The GenABEL documentation explains this
+procedure in more detail.
+
An example of how a polygenic object estimated by \GA{} can be used
with ProbABEL is provided in \texttt{examples/mmscore.R}
@@ -799,7 +825,7 @@
\end{quote}
A proper reference may look like
\begin{quote}
-For the analysis of imputed data, we used the \PA{}
+For the analysis of imputed data, we used the \PA{} v.0.2.0
from the \texttt{GenABEL} suite of programs (Aulchenko \emph{et al.}, 2010).
\end{quote}
Modified: branches/ProbABEL-refactoring/ProbABEL/doc/packaging.txt
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/doc/packaging.txt 2012-10-24 10:15:58 UTC (rev 985)
+++ branches/ProbABEL-refactoring/ProbABEL/doc/packaging.txt 2012-10-24 10:18:55 UTC (rev 986)
@@ -13,18 +13,18 @@
in the automake files:
./configure
make distcheck
- If there are no errors, a tar.gz file of the source should be
+ If there are no errors, a tar.gz file of the source should have been
created. Let's create the package.
mkdir /tmp/PA-deb
- cp ProbABEL-0.2.0-beta.tar.gz /tmp/PA-deb
+ cp ProbABEL-0.2.0.tar.gz /tmp/PA-deb
cd /tmp/PA-deb
Debian packages must have lowercase letters, so we'll have to rename
the directory after untar-ing it.
- tar -xzf ProbABEL-0.2.0-beta.tar.gz
- mv ProbABEL-0.2.0-beta probabel-0.2-0-beta
- cd probabel-0.2.0-beta
+ tar -xzf ProbABEL-0.2.0.tar.gz
+ mv ProbABEL-0.2.0 probabel-0.2-0
+ cd probabel-0.2.0
dh_make --single --email youremail at example.com \
- --file ../ProbABEL-0.2.0-beta.tar.gz --copyright gpl2 \
+ --file ../ProbABEL-0.2.0.tar.gz --copyright gpl2 \
--packagename probabel
Hit the enter key to confirm the settings. Several files need to be
@@ -35,12 +35,13 @@
- debian/README.Debian
dh_make also creates several example scripts in the debian/
directory. We don't need them, so they can be delete:
- rm debian/*.ex
- Now the package can be built:
+ rm debian/*.ex debian/*.EX
+ Now the package can be built (NOTE that dpkg-buildpackage replaces
+ our default CXXFLAGS with "-g -O2"):
dpkg-buildpackage -rfakeroot -us -uc
- This creates a ~.deb~ file in the parent directory. As a
+ This creates an unsigned ~.deb~ file in the parent directory. As a
final touch you can check you package for errors with
- lintian ../probabel_0.2.0-beta-1_amd64.deb
+ lintian ../probabel_0.2.0-1_amd64.deb
Several warnings will show up (e.g. binaries without man-pages),
but we ignore these for now. If you are interested in a more
detailed explanation of the warnings, add the -i option to the
@@ -48,3 +49,10 @@
These last two commands can be run in one go using debuild (which
is part of the devscripts package):
debuild -i -us -uc -b
+** Uploading to an Ubuntu PPA (Personal Package Archive)
+ Building a package for upload to a PPA is almost the same as shown above:
+ debuild -i -S -kYOURKEYID
+ where YOURKEYID is the ID of the gpg key you use for signing your
+ package (this key should be known by launchpad).
+ To upload the package created above to the GenABEL PPA simply type:
+ dput ppa:l.c.karssen/genabel-ppa ../probabel_0.2.0-1_source.changes
Modified: branches/ProbABEL-refactoring/ProbABEL/doc/palinear.1
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/doc/palinear.1 2012-10-24 10:15:58 UTC (rev 985)
+++ branches/ProbABEL-refactoring/ProbABEL/doc/palinear.1 2012-10-24 10:18:55 UTC (rev 986)
@@ -17,60 +17,60 @@
.BI "\-i, \-\^\-info" " FILE"
Read SNP information from
.I FILE
-(e.g. MLINFO file)
+(e.g. MLINFO file).
.TP
.BI "\-d, \-\^\-dose" " FILE"
-SNP predictor (e.g. MLDOSE/MLPROB) file name
+SNP predictor (e.g. MLDOSE/MLPROB) file name.
.SS Optional command line options
.TP
.BI "\-\^\-map" " FILE"
Map file name, containing base pair positions for each SNP.
.TP
.BI "\-\^\-nids" " NUMBER"
-Number of people to analyse
+Number of people to analyse.
.TP
.BI "\-\^\-chrom" " FILE"
-Chromosome (to be passed to output)
+Chromosome (to be passed to output).
.TP
.BI "\-\^\-out" " FILE"
Output file name (default is
.B regression.out.txt
-)
+).
.TP
.BI "\-\^\-skipd" " NUMBER"
-How many columns to skip in predictor (dose/prob) file (default is 2)
+How many columns to skip in predictor (dose/prob) file (default is 2).
.TP
.BI "\-\^\-ntraits" " NUMBER"
-How many traits are analysed (default is 1)
+How many traits are analysed (default is 1).
.TP
.BI "\-\^\-ngpreds" " NUMBER"
-How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB)
+How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB).
.TP
.B "\-\^\-separat" " FILE"
-Character to separate fields (default is space)
+Character to separate fields (default is space).
.TP
.B \-\^\-score
-Use the score test
+Use the score test.
.TP
.B \-\^\-no-head
-Do not report header line in the output
+Do not report header line in the output.
.TP
.B \-\^\-allcov
-Report estimates for all covariates (large outputs!)
+Report estimates for all covariates (large outputs!).
.TP
.B \-\^\-interaction
-Which covariate to use for interaction with SNP analysis (default is no interaction, 0)
+Which covariate to use for interaction with SNP analysis (default is no interaction, 0).
.TP
.B \-\^\-interaction_only
Like
.B \-\^\-interaction
-but without covariate acting in interaction with SNP (default is no interaction, 0)
+but without covariate acting in interaction with SNP (default is no interaction, 0).
.TP
.BI "\-\^\-mmscore" " FILE"
-Score test in samples of related individuals. File with inverse of variance-covariance matrix (for palinear) or inverse correlation (for palogist) as input parameter
+Score test in samples of related individuals. The FILE argument is the name of a file with the inverse of the variance-covariance matrix.
.TP
.B \-\^\-robust
-Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors
+Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors.
.TP
.B \-\^\-help
Print help
Modified: branches/ProbABEL-refactoring/ProbABEL/doc/palogist.1
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/doc/palogist.1 2012-10-24 10:15:58 UTC (rev 985)
+++ branches/ProbABEL-refactoring/ProbABEL/doc/palogist.1 2012-10-24 10:18:55 UTC (rev 986)
@@ -17,63 +17,63 @@
.BI "\-i, \-\^\-info" " FILE"
Read SNP information from
.I FILE
-(e.g. MLINFO file)
+(e.g. MLINFO file).
.TP
.BI "\-d, \-\^\-dose" " FILE"
-SNP predictor (e.g. MLDOSE/MLPROB) file name
+SNP predictor (e.g. MLDOSE/MLPROB) file name.
.SS Optional command line options
.TP
.BI "\-\^\-map" " FILE"
Map file name, containing base pair positions for each SNP.
.TP
.BI "\-\^\-nids" " NUMBER"
-Number of people to analyse
+Number of people to analyse.
.TP
.BI "\-\^\-chrom" " FILE"
-Chromosome (to be passed to output)
+Chromosome (to be passed to output).
.TP
.BI "\-\^\-out" " FILE"
Output file name (default is
.B regression.out.txt
-)
+).
.TP
.BI "\-\^\-skipd" " NUMBER"
-How many columns to skip in predictor (dose/prob) file (default is 2)
+How many columns to skip in predictor (dose/prob) file (default is 2).
.TP
.BI "\-\^\-ntraits" " NUMBER"
-How many traits are analysed (default is 1)
+How many traits are analysed (default is 1).
.TP
.BI "\-\^\-ngpreds" " NUMBER"
-How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB)
+How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB).
.TP
.B "\-\^\-separat" " FILE"
-Character to separate fields (default is space)
+Character to separate fields (default is space).
.TP
.B \-\^\-score
-Use the score test
+Use the score test.
.TP
.B \-\^\-no-head
-Do not report header line in the output
+Do not report header line in the output.
.TP
.B \-\^\-allcov
-Report estimates for all covariates (large outputs!)
+Report estimates for all covariates (large outputs!).
.TP
.B \-\^\-interaction
-Which covariate to use for interaction with SNP analysis (default is no interaction, 0)
+Which covariate to use for interaction with SNP analysis (default is no interaction, 0).
.TP
.B \-\^\-interaction_only
Like
.B \-\^\-interaction
-but without covariate acting in interaction with SNP (default is no interaction, 0)
+but without covariate acting in interaction with SNP (default is no interaction, 0).
.TP
.BI "\-\^\-mmscore" " FILE"
-Score test in samples of related individuals. File with inverse of variance-covariance matrix (for palogist) or inverse correlation (for palogist) as input parameter
+Score test in samples of related individuals. The FILE argument is the name of a file with the inverse correlation matrix. NOTE THAT THIS FEATURE IS STILL EXPERIMENTAL!
.TP
.B \-\^\-robust
-Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors
+Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors.
.TP
.B \-\^\-help
-Print help
+Print help.
.SH "SEE ALSO"
palinear(1), pacoxph(1)
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