[Genabel-commits] r914 - in pkg/ProbABEL: . doc src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Jun 10 22:43:24 CEST 2012
Author: lckarssen
Date: 2012-06-10 22:43:24 +0200 (Sun, 10 Jun 2012)
New Revision: 914
Modified:
pkg/ProbABEL/configure.ac
pkg/ProbABEL/doc/CHANGES.LOG
pkg/ProbABEL/doc/ProbABEL_manual.tex
pkg/ProbABEL/src/Makefile.am
Log:
- Updated version number to 0.2.0. Unless I find showstoppers this will be tagged as ProbABEL 0.2.0 (configure.ac and doc/ProbABEL_manual.tex)
- Updated documentation to include info about the mmscore option for palogist
- Set the default CXXFLAGS to -g -O3 as they were in the previous released version of ProbABEL.
- Set the default CPPFLAGS to -Wall. We want clean code that follows the standard :-). (configure.ac and src/Makefile.am)
Modified: pkg/ProbABEL/configure.ac
===================================================================
--- pkg/ProbABEL/configure.ac 2012-06-10 19:15:17 UTC (rev 913)
+++ pkg/ProbABEL/configure.ac 2012-06-10 20:43:24 UTC (rev 914)
@@ -2,17 +2,27 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ([2.67])
-AC_INIT(ProbABEL, 0.1.99, genabel-devel at r-forge.wu-wien.ac.at)
-AM_INIT_AUTOMAKE(ProbABEL, 0.1.99)
+AC_INIT(ProbABEL, 0.2.0, genabel-devel at r-forge.wu-wien.ac.at)
+AM_INIT_AUTOMAKE(ProbABEL, 0.2.0)
AC_CONFIG_SRCDIR([src/data.h])
AC_CONFIG_HEADERS([src/config.h])
# Checks for programs.
-AC_PROG_CXX
AC_PROG_CC
AM_PROG_CC_C_O
AC_PROG_INSTALL
AC_PROG_LN_S
+if test -z "$CXXFLAGS"; then
+ # User did not set CXXFLAGS, so we can put in our own defaults
+ CXXFLAGS="-g -O3"
+fi
+if test -z "$CPPFLAGS"; then
+ # User did not set CXXFLAGS, so we can put in our own defaults
+ CPPFLAGS="-Wall"
+fi
+# If CXXFLAGS/CPPFLAGS are already set AC_PROG_CXX will not overwrite them
+# with its own defaults
+AC_PROG_CXX
# Checks for libraries.
Modified: pkg/ProbABEL/doc/CHANGES.LOG
===================================================================
--- pkg/ProbABEL/doc/CHANGES.LOG 2012-06-10 19:15:17 UTC (rev 913)
+++ pkg/ProbABEL/doc/CHANGES.LOG 2012-06-10 20:43:24 UTC (rev 914)
@@ -1,22 +1,23 @@
-***** v.0.2-0 (2012.03.04)
+***** 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.
+ ./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$estimate)]
-where h2.object is the object returned by 'polygenic()'. Documentation
-explains this procedure in more details; a wrapper function to prepare
-and export correct objects for ProbABEL is planned. (thanks to Yurii)
+ where h2.object is the object returned by 'polygenic()'. Documentation
+ explains this procedure in more details; a wrapper function to prepare
+ and export correct objects for ProbABEL is planned. (thanks to Yurii)
* Small changes (thanks to Lennart).
- in probabel.pl the location for the probabel config file is now set
Modified: pkg/ProbABEL/doc/ProbABEL_manual.tex
===================================================================
--- pkg/ProbABEL/doc/ProbABEL_manual.tex 2012-06-10 19:15:17 UTC (rev 913)
+++ pkg/ProbABEL/doc/ProbABEL_manual.tex 2012-06-10 20:43:24 UTC (rev 914)
@@ -1,4 +1,4 @@
-\title{ProbABEL manual}
+\title{Manual for ProbABEL v0.2.0}
\author{
Maksim Struchalin$^{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}
@@ -261,8 +265,13 @@
\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 +281,7 @@
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:
@@ -330,7 +339,12 @@
-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 +380,27 @@
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-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.
+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}
Modified: pkg/ProbABEL/src/Makefile.am
===================================================================
--- pkg/ProbABEL/src/Makefile.am 2012-06-10 19:15:17 UTC (rev 913)
+++ pkg/ProbABEL/src/Makefile.am 2012-06-10 20:43:24 UTC (rev 914)
@@ -24,8 +24,6 @@
include/R_ext/Print.h include/R_ext/Random.h include/R_ext/Utils.h \
include/R_ext/RS.h
-AM_CXXFLAGS = -Wall -O3
-
bin_PROGRAMS = palinear palogist
if BUILD_pacoxph
## Extra files for pacoxph
@@ -37,13 +35,16 @@
palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
palinear_CXXFLAGS = -DLINEAR $(AM_CXXFLAGS)
+palinear_CPPFLAGS = $(AM_CPPFLAGS)
palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
palogist_CXXFLAGS = -DLOGISTIC $(AM_CXXFLAGS)
+palogist_CPPFLAGS = $(AM_CPPFLAGS)
pacoxph_SOURCES = $(COXSRC) $(REGFILES) $(FVSRC) $(FVHEADERS) \
$(RHEADERS) survS.h survproto.h
pacoxph_CXXFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CXXFLAGS)
+pacoxph_CPPFLAGS = $(AM_CPPFLAGS)
pacoxph_CFLAGS = -DCOXPH -I $(top_srcdir)/src/include $(AM_CFLAGS)
## Install these scripts in the bin directory as well:
More information about the Genabel-commits
mailing list