[GenABEL-dev] [Genabel-commits] r759 - in pkg/ProbABEL: doc src
Yury Aulchenko
yurii.aulchenko at gmail.com
Wed Aug 17 13:36:46 CEST 2011
This is indeed small but useful update of documentation, thanks, Lennart!
best wishes,
Yurii
On Aug 12, 2011, at 10:06 AM, noreply at r-forge.wu-wien.ac.at wrote:
> Author: lckarssen
> Date: 2011-08-12 10:06:43 +0200 (Fri, 12 Aug 2011)
> New Revision: 759
>
> Removed:
> pkg/ProbABEL/src/version.h
> Modified:
> pkg/ProbABEL/doc/ProbABEL_manual.tex
> pkg/ProbABEL/src/Makefile.am
> pkg/ProbABEL/src/Makefile.in
> pkg/ProbABEL/src/main.cpp
> Log:
> - Fixed bug $1290: usage of DatABEL files not explained in the
> manual. See also http://forum.genabel.org/viewtopic.php?f=6&t=22 for
> some discussion.
> - Since we now use autoconf, which generates src/config.h, we don't
> need a separate src/version.h anymore. When upgrading the version of
> ProbABEL, simply do it in configure.ac and the change will be
> automatically trickle down to main.cpp.
>
>
>
> Modified: pkg/ProbABEL/doc/ProbABEL_manual.tex
> ===================================================================
> --- pkg/ProbABEL/doc/ProbABEL_manual.tex 2011-08-11 22:41:45 UTC (rev 758)
> +++ pkg/ProbABEL/doc/ProbABEL_manual.tex 2011-08-12 08:06:43 UTC (rev 759)
> @@ -93,13 +93,6 @@
> Optionally, the map information can be supplied (e.g.~the "legend"
> files of HapMap).
>
> -The dose/probbaility file may be supplied in filevector format
> -in which case \texttt{ProbABEL} will operate much faster, and
> -in low-RAM mode (approx.~128 MB). See the R libraries GenABEL and
> -DatABEL on how to convert MACH and IMPUTE files to
> -filevector format (functions: \texttt{mach2databel()} and
> -\texttt{impute2databel()}, respectively).
> -
> \subsection{SNP information file}
> \label{ssec:infoin}
> In the simplest scenario, the SNP information file is an MLINFO
> @@ -149,6 +142,18 @@
> Therefore, by all means, the number of columns in the genomic predictor file
> must be the same as the number of lines in the SNP information file plus one.
>
> +The dose/probability file may be supplied in filevector format
> +(\texttt{.fvi} and \texttt{.fvd} files) in which case
> +\texttt{ProbABEL} will operate much faster, and in low-RAM mode
> +(approx.~128 MB). On the command line simply specify the \texttt{.fvi}
> +file as argument for the \texttt{--dose} option
> +(cf.~section~\ref{sec:runanalysis} for more information on the options
> +accepted by \texttt{ProbABEL}). See the R libraries GenABEL and
> +DatABEL on how to convert MACH and IMPUTE files to filevector format
> +(functions: \texttt{mach2databel()} and \texttt{impute2databel()},
> +respectively).
> +
> +
> \subsection{Phenotypic file}
> \label{ssec:phenoin}
>
> @@ -226,6 +231,7 @@
> actually used to generate the output.
>
> \section{Running an analysis}
> +\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
>
> Modified: pkg/ProbABEL/src/Makefile.am
> ===================================================================
> --- pkg/ProbABEL/src/Makefile.am 2011-08-11 22:41:45 UTC (rev 758)
> +++ pkg/ProbABEL/src/Makefile.am 2011-08-12 08:06:43 UTC (rev 759)
> @@ -3,7 +3,7 @@
> ## Using wildcards in these lists doesn't work. Also GNU make's ($wildcard,) doesn't
> ## work. It gives warning message about portability, but in the end doesn't work,
> ## I tried :-).
> -REGFILES = data.h mematrix.h reg1.h usage.h main.cpp mematri1.h version.h
> +REGFILES = data.h mematrix.h reg1.h usage.h main.cpp mematri1.h
>
> ## Filevector files:
> FVSRC = fvlib/AbstractMatrix.cpp fvlib/CastUtils.cpp \
>
> Modified: pkg/ProbABEL/src/Makefile.in
> ===================================================================
> --- pkg/ProbABEL/src/Makefile.in 2011-08-11 22:41:45 UTC (rev 758)
> +++ pkg/ProbABEL/src/Makefile.in 2011-08-12 08:06:43 UTC (rev 759)
> @@ -234,7 +234,7 @@
> top_build_prefix = @top_build_prefix@
> top_builddir = @top_builddir@
> top_srcdir = @top_srcdir@
> -REGFILES = data.h mematrix.h reg1.h usage.h main.cpp mematri1.h version.h
> +REGFILES = data.h mematrix.h reg1.h usage.h main.cpp mematri1.h
> FVSRC = fvlib/AbstractMatrix.cpp fvlib/CastUtils.cpp \
> fvlib/convert_util.cpp fvlib/FileVector.cpp fvlib/FilteredMatrix.cpp \
> fvlib/frutil.cpp fvlib/Logger.cpp fvlib/RealHandlerWrapper.cpp \
>
> Modified: pkg/ProbABEL/src/main.cpp
> ===================================================================
> --- pkg/ProbABEL/src/main.cpp 2011-08-11 22:41:45 UTC (rev 758)
> +++ pkg/ProbABEL/src/main.cpp 2011-08-12 08:06:43 UTC (rev 759)
> @@ -9,7 +9,8 @@
> // Revision: none
> //
> // Author: Yurii S. Aulchenko (cox, log, lin regressions)
> -// Modified by: Maksim V. Struchalin,
> +// Modified by: L.C. Karssen,
> +// Maksim V. Struchalin
> //
> // modified 14-May-2009 by MVS: interaction with SNP, interaction with SNP with exclusion of interacted covariates,
> // mmscore implemented (poor me)
> @@ -38,7 +39,7 @@
> #include <sstream>
>
>
> -#include "version.h"
> +#include "config.h"
> #include "mematrix.h"
> #include "mematri1.h"
> #include "data.h"
> @@ -184,7 +185,11 @@
> while (next_option != -1);
>
>
> - fprintf(stdout,"ProbABEL v. %s (%s) (C) Yurii Aulchenko, Maksim Struchalin, EMCR\n\n",VERSION,DATE);
> + fprintf(stdout,
> + "%s v. %s (C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, EMCR\n\n",
> + PACKAGE,
> + PACKAGE_VERSION);
> +
> if (neco[0]!=1 || neco[1]!=1 || neco[2]!=1)
> {
> print_usage(program_name,1);
>
> Deleted: pkg/ProbABEL/src/version.h
> ===================================================================
> --- pkg/ProbABEL/src/version.h 2011-08-11 22:41:45 UTC (rev 758)
> +++ pkg/ProbABEL/src/version.h 2011-08-12 08:06:43 UTC (rev 759)
> @@ -1,2 +0,0 @@
> -#define VERSION "0.1-9e"
> -#define DATE "May 15, 2011"
>
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