[GenABEL-dev] [Genabel-commits] r762 - in pkg/ProbABEL: doc src

[L.C. Karssen]

On di, 2011-08-23 at 22:14 +0200, Yury Aulchenko wrote:
> Dear Lennart,
Hi Yurii,

> 
> 
> You did terrific job converting ProbABEL in quite professional-looking
> product!

Thanks a lot! My pleasure.

> 
> 
> I have just committed few changes related to documentation and adding
> '--mmscore' option for binary traits; also changed version to 0.2-0 as
> you suggested. Seems all worked all right, though I had to merge few
> files. 
> 
> 
> One questions: what is the right way to clean up local source before
> committing? It seems that a number of newly generated files
> (Makefile's,srd/.deps ...) hang around after running 'make
> clean' (naturally). I can just force them to be ignored by commit, but
> wonder if there may be a more proper way to do this?

Yes, simply run
make distclean

That is the default target to clean everything up (as if ./configure was
never run at all).


Best regards,

Lennart.

> 
> 
> best wishes,
> Yurii
> -------------------------------------------------------
> Yurii Aulchenko, PhD, Dr. Habil.
> Independent researcher and consultant
> yurii [dot] aulchenko [at] gmail [dot] com
> 
> On Aug 23, 2011, at 9:48 PM, noreply at r-forge.wu-wien.ac.at wrote:
> 
> > Author: yurii
> > Date: 2011-08-23 21:48:36 +0200 (Tue, 23 Aug 2011)
> > New Revision: 762
> > 
> > Modified:
> >   pkg/ProbABEL/doc/CHANGES.LOG
> >   pkg/ProbABEL/doc/ProbABEL_manual.tex
> >   pkg/ProbABEL/src/main.cpp
> >   pkg/ProbABEL/src/mematri1.h
> >   pkg/ProbABEL/src/reg1.h
> >   pkg/ProbABEL/src/usage.h
> > Log:
> > update manual; changes.log; add '--mmscore' option for binary traits
> > 
> > Modified: pkg/ProbABEL/doc/CHANGES.LOG
> > ===================================================================
> > --- pkg/ProbABEL/doc/CHANGES.LOG 2011-08-22 08:32:43 UTC (rev 761)
> > +++ pkg/ProbABEL/doc/CHANGES.LOG 2011-08-23 19:48:36 UTC (rev 762)
> > @@ -1,3 +1,54 @@
> > +***** v.0.2-0 (2011.08.23)
> > +
> > +* 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: on the contrast to the 
> > +'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$InvSigma * h.object2$h2an$estimate[length(h2$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) 
> > +
> > +- in probabel.pl the location for the probabel config file is now
> > set
> > +  to /etc/, the default location it will end up. Before it still
> > +  pointed to the location the probabel.pl file was in. However, a
> > +  better fix would be to somehow put in the actual value of the
> > +  --sysconfdir option to ./configure.
> > +- 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.
> > +
> > +
> > +* ProbABEL uses autoconf and automake now (thanks to Lennart). Now
> > the 
> > +compilation process is like this: first, from the ProbABEL
> > directory, 
> > +generate documentation by
> > +
> > +cd doc
> > +make
> > +make clean_doc
> > +cd ..
> > +
> > +Then, run
> > +
> > +./configure
> > +make
> > +make install 
> > +
> > +To see options, run
> > +
> > +./configure --help
> > +
> > +In the ProbABEL autotools integration branch:
> > +- Removed the old Makefile
> > +- Added configure.ac that servers as input for auto(re)conf
> > +- Added the Makefile.am files needed by automake to generate the
> > final Makefiles.
> > +
> > +
> > ***** v.0.1-9e (2011.05.15)
> > Previous version wouldn't compile because of missing frerror. file.
> > Fixes bug #1339 (the bug fix was done a month ago, but no package
> > had
> > 
> > Modified: pkg/ProbABEL/doc/ProbABEL_manual.tex
> > ===================================================================
> > --- pkg/ProbABEL/doc/ProbABEL_manual.tex 2011-08-22 08:32:43 UTC
> > (rev 761)
> > +++ pkg/ProbABEL/doc/ProbABEL_manual.tex 2011-08-23 19:48:36 UTC
> > (rev 762)
> > @@ -1,6 +1,9 @@
> > \title{ProbABEL manual}
> > -\author{Yurii Aulchenko, Maksim Struchalin, Lennart Karssen \\
> > - Erasmus MC Rotterdam
> > +\author{
> > +Maksim Struchalin$^{1}$, Lennart Karssen$^{1}$, Yurii Aulchenko
> > $^{1,2}$ \\ 
> > +\\
> > +$^{1}$Erasmus MC Rotterdam \\ 
> > +$^{2}$Institute of Cytology and Genetics SD RAS 
> > }
> > \date{\today}
> > 
> > @@ -28,6 +31,10 @@
> > 
> > \makeindex
> > 
> > +\newcommand{\PA}{\texttt{ProbABEL-package}}
> > +\newcommand{\GA}{\texttt{GenABEL-package}}
> > +\newcommand{\DA}{\texttt{DatABEL-package}}
> > +
> > \begin{document}
> > \maketitle
> > \tableofcontents
> > @@ -76,16 +83,16 @@
> > performing association analysis by means of regression of the
> > outcome of interest onto estimated genotypic probabilities.
> > 
> > -The \texttt{ProbABEL} package was designed to perform such
> > regression
> > +The \PA{} package was designed to perform such regression
> > in a fast, memory-efficient and consequently genome-wide feasible
> > manner.
> > -Currently, \texttt{ProbABEL} implements linear, logistic
> > regression,
> > +Currently, \PA{} implements linear, logistic regression,
> > and Cox proportional hazards models. The corresponding analysis
> > programs are called \texttt{palinear},  \texttt{palogist},
> > and \texttt{pacoxph}.
> > 
> > 
> > \section{Input files}
> > -\texttt{ProbABEL} takes three files as input: a file containing SNP
> > +\PA{} takes three files as input: a file containing SNP
> > information (e.g.~the MLINFO file of MACH), a file with genome- or
> > chromosome-wide predictor information (e.g.~the MLDOSE or MLPROB
> > file of MACH),
> > and a file containing the phenotype of interest and covariates.
> > @@ -93,6 +100,13 @@
> > Optionally, the map information can be supplied (e.g.~the "legend"
> > files of HapMap).
> > 
> > +The dose/probability file may be supplied in filevector format
> > +in which case \PA{} will operate much faster, and
> > +in low-RAM mode (approx. $\approx$ 128 MB). See the R libraries
> > \GA{} and
> > +\DA{} 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
> > @@ -103,7 +117,7 @@
> > ``Rsq'', the proportion of variance decrease after imputations).
> > 
> > Actually,
> > -for \texttt{ProbABEL}, it does not matter what is written in this
> > file --
> > +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
> > @@ -239,7 +253,7 @@
> > the program).
> > 
> > There are in total 11 command line options you can specify to the
> > -\texttt{ProbABEL} analysis functions \texttt{palinear} or
> > +\PA{} analysis functions \texttt{palinear} or
> > \texttt{palogist}. If you run either program without any argument,
> > you
> > will get a short explanation to command line options:
> > \begin{verbatim}
> > @@ -350,25 +364,25 @@
> > first column contains id names, the second the trait. The others are
> > covariates.
> > 
> > -An example of how a polygenic object estimated by GenABEL can be
> > used
> > +An example of how a polygenic object estimated by \GA{} can be used
> > with ProbABEL is provided in \texttt{../example/mmscore.R}
> > 
> > Though technically \texttt{--mmscore} allows for inclusion of
> > multiple
> > covariates, these should be kept to minimum as this is a score test.
> > We
> > suggest that any covariates explaining an essential proportion of
> > -variance should be fit as part of \texttt{GenABEL}'s
> > +variance should be fit as part of \GA{}'s
> > \texttt{polygenic} procedure.
> > 
> > %Option \texttt{--interaction\_only} is like \texttt{--interaction}
> > but does not
> > %include in the model the main effect of the covariate, which is
> > acting in
> > %interaction with SNP. This option is useful when running
> > \texttt{--mmscore},
> > %in whch case the main effect should normally estimated in the
> > polygenic
> > -%model and only the interaction term in the \texttt{ProbABEL}
> > analysis.
> > +%model and only the interaction term in the \PA{} analysis.
> > 
> > \subsection{Running multiple analyses at once: \texttt{probabel.pl}}
> > 
> > The Perl script \texttt{bin/probabel.pl\_example} represents a handy
> > -wraper for \texttt{ProbABEL} functions.  To start using it the
> > +wraper for \PA{} functions.  To start using it the
> > configuration file \texttt{bin/probabel\_config.cfg\_example} needs
> > to
> > be edited. The configuration file consists of five columns. Each
> > column except the first is a pattern for files produced by
> > @@ -383,7 +397,7 @@
> > for the ``mlinfo'' files. Probably you also have to change the
> > variable
> > \texttt{\$config} in the script to point to the full path of the
> > configuration file and the variable \texttt{@anprog} to point full
> > -path to the \texttt{ProbABEL} scripts.
> > +path to the \PA{} scripts.
> > 
> > 
> > \section{Output file format}
> > @@ -412,7 +426,7 @@
> > At this point, unless you have complete measurements on all
> > subjects, you should feel alarmed if the number here is exactly the
> > number of people in the file -- this probably indicates you did not
> > code
> > -missing values according to \texttt{ProbABEL} format ('NA', 'NaN',
> > or 'N').
> > +missing values according to \PA{} format ('NA', 'NaN', or 'N').
> > 
> > The next column, nine (``Mean\_predictor\_allele''), gives the
> > estimated
> > frequency of the predictor allele in subjects with complete
> > phenotypic data.
> > @@ -433,14 +447,24 @@
> > 
> > \section{Memory use and performance}
> > Maximum likelihood regression is implemented in
> > -\texttt{ProbABEL}. With 6,000 people and 2.5 millions SNPs, a
> > +\PA{}. With 6,000 people and 2.5 millions SNPs, a
> > genome-wide scan is completed in less that an hour for a linear
> > model
> > with 1-2 covariates and overnight for logistic regression or the Cox
> > -proportional hazards model.
> > +proportional hazards model (figures for a PC bought back in 2007).
> > 
> > -Memory is an issue with \texttt{ProbABEL} -- large chromosomes,
> > +Memory may be an issue with \PA{} if you use 
> > +MACH text dose/probability files, e.g. for large chromosomes,
> > such as chromosome one consumed up to 5 GB of RAM with 6,000 people.
> > 
> > +We suggest that dose/probability file is to be supplied in
> > filevector format
> > +in which case \PA{} will operate about 2-3 times faster, and
> > +in low-RAM mode (approx.~128 MB). See the R libraries \GA{} and
> > +\DA{} on how to convert MACH and IMPUTE files to
> > +filevector format (functions: \texttt{mach2databel()} and
> > +\texttt{impute2databel()}, respectively).
> > +
> > +When '--mmscore' option is used, the analysis may take quite some
> > time. 
> > +
> > \section{Methodology}
> > \label{sec:methodology}
> > \subsection{Analysis of population-based data}
> > @@ -598,7 +622,7 @@
> > \index{Cox proportional hazards model}
> > \index{proportional hazards model}
> > \index{regression!Cox proportional hazards}
> > -in \texttt{ProbABEL} is entirely based on the code of \texttt{R}
> > +in \PA{} is entirely based on the code of \texttt{R}
> > library \texttt{survival} developed by Thomas Lumley
> > (function \texttt{coxfit2}), and is therefore not described here.
> > 
> > @@ -742,14 +766,14 @@
> > 
> > \section{How to cite}
> > 
> > -If you used \texttt{ProbABEL} for
> > -your analysis please give a link to the \texttt{ABEL} home
> > +If you used \PA{} for
> > +your analysis please give a link to the \texttt{GenABEL project}
> > home
> > page
> > 
> > \begin{quote}
> > \url{http://www.genabel.org/}
> > \end{quote}
> > -and cite the \texttt{ProbABEL} paper to give us some credit:
> > +and cite the \PA{} paper to give us some credit:
> > \begin{quote}
> > Aulchenko YS, Struchalin MV, van Duijn CM.\\
> > \emph{ProbABEL package for genome-wide association analysis of
> > imputed data.}\\
> > @@ -757,15 +781,15 @@
> > \end{quote}
> > A proper reference may look like
> > \begin{quote}
> > -For the analysis of imputed data, we used the \texttt{ProbABEL}
> > package
> > -from the GenABEL suite of programs (Aulchenko \emph{et al.}, 2010).
> > +For the analysis of imputed data, we used the \PA{} 
> > +from the \texttt{GenABEL} suite of programs (Aulchenko \emph{et
> > al.}, 2010).
> > \end{quote}
> > 
> > If you have used the Cox proportional hazard model, please mention
> > the
> > \texttt{R} package \texttt{survival} by Thomas Lumley. Additionally
> > to the above citation, please tell that
> > \begin{quote}
> > -The Cox proportional hazards model implemented in \texttt{ProbABEL}
> > +The Cox proportional hazards model implemented in \PA{}
> > makes use of the source code of the \texttt{R} package
> > ''\texttt{survival}''
> > as implemented by T. Lumley.
> > \end{quote}
> > 
> > Modified: pkg/ProbABEL/src/main.cpp
> > ===================================================================
> > --- pkg/ProbABEL/src/main.cpp 2011-08-22 08:32:43 UTC (rev 761)
> > +++ pkg/ProbABEL/src/main.cpp 2011-08-23 19:48:36 UTC (rev 762)
> > @@ -303,9 +303,12 @@
> > 
> > mematrix<double> invvarmatrix;
> > 
> > +/*
> > + * now should be possible... delete this part later when everything
> > works
> > #if LOGISTIC 
> > if(inverse_filename != NULL) {std::cerr<<"ERROR: mmscore is
> > forbidden for logistic regression\n";exit(1);}
> > #endif
> > +*/
> > 
> > #if COXPH
> > if(inverse_filename != NULL) {std::cerr<<"ERROR: mmscore is
> > forbidden for cox regression\n";exit(1);}
> > 
> > Modified: pkg/ProbABEL/src/mematri1.h
> > ===================================================================
> > --- pkg/ProbABEL/src/mematri1.h 2011-08-22 08:32:43 UTC (rev 761)
> > +++ pkg/ProbABEL/src/mematri1.h 2011-08-23 19:48:36 UTC (rev 762)
> > @@ -368,7 +368,7 @@
> >   {
> > if (M.ncol != M.nrow) 
> > {
> > - fprintf(stderr,"invert: only suare matrices possible\n");
> > + fprintf(stderr,"invert: only square matrices possible\n");
> > exit(1);
> > }
> > if (M.ncol == 1) 
> > @@ -376,12 +376,19 @@
> > mematrix<DT> temp(1,1);
> > temp[0] = 1./M[0];
> > }
> > + /*
> > for (int i=0;i<M.ncol;i++) 
> > if (M.data[i*M.ncol+i]==0) 
> > {
> > fprintf(stderr,"invert: zero elements in diagonal\n");
> > - exit(1);
> > + mematrix<DT> temp = M;
> > + for (int i = 0; i < M.ncol; i++)
> > + for (int j = 0; j < M.ncol; j++)
> > + temp.put(NAN,i,j);
> > + return temp;
> > + //exit(1);
> > }
> > + */
> > int actualsize = M.ncol;
> > int maxsize = M.ncol;
> > mematrix<DT> temp = M;
> > 
> > Modified: pkg/ProbABEL/src/reg1.h
> > ===================================================================
> > --- pkg/ProbABEL/src/reg1.h 2011-08-22 08:32:43 UTC (rev 761)
> > +++ pkg/ProbABEL/src/reg1.h 2011-08-23 19:48:36 UTC (rev 762)
> > @@ -626,7 +626,7 @@
> > //Oct 26, 2009
> > residuals.reinit((rdata.X).nrow,1);
> > sigma2=-1.;
> > - loglik=-9.999e+32;
> > + loglik=-9.999e+32; // should actually be MAX of the corresponding
> > type
> > niter=-1;
> > chi2_score=-1.;
> > }
> > @@ -635,10 +635,36 @@
> > // delete beta;
> > // delete sebeta;
> > }
> > - void estimate(regdata &rdatain, int verbose, int maxiter, double
> > eps, double tol_chol, int model, int interaction, int ngpreds,
> > mematrix<double> & invvarmatrix, int robust, int nullmodel=0)
> > +
> > + void estimate(regdata &rdatain, int verbose, int maxiter, double
> > eps, double tol_chol,
> > + int model, int interaction, int ngpreds, mematrix<double> &
> > invvarmatrixin, int robust,
> > + int nullmodel=0)
> > {
> > + // on the contrast to the 'linear' 'invvarmatrix' contains
> > + // inverse of correlation matrix (not the inverse of var-cov
> > matrix)
> > + // h2.object$InvSigma * h.object2$h2an$estimate[length(h2$h2an
> > $estimate)]
> > + // the inverse of var-cov matrix scaled by total variance
> > regdata rdata = rdatain.get_unmasked_data();
> > 
> > + // a lot of code duplicated between linear and logistic...
> > + // e.g. a piece below...
> > + mematrix<double> invvarmatrix;
> > + if(invvarmatrixin.nrow!=0 && invvarmatrixin.ncol!=0)
> > + {
> > + invvarmatrix.reinit(rdata.nids,rdata.nids);
> > + int i1=0, j1=0;
> > + for (int i=0;i<rdata.nids;i++)
> > + if (rdatain.masked_data[i]==0) {
> > + j1 = 0;
> > + for (int j=0;j<rdata.nids;j++) if (rdatain.masked_data[j]==0) {
> > + invvarmatrix.put(invvarmatrixin.get(i,j),i1,j1);
> > + j1++;
> > + }
> > + i1++;
> > + }
> > +
> > + }
> > +
> > mematrix<double> X = apply_model(rdata.X,model, interaction,
> > ngpreds, false, nullmodel);
> > int length_beta = X.ncol;
> > beta.reinit(length_beta,1);
> > @@ -668,10 +694,20 @@
> > 
> > mematrix<double> tX = transpose(X);
> > 
> > - // if(invvarmatrix.nrow!=0 && invvarmatrix.ncol!=0) tX =
> > X*invvarmatrix;
> > + if(invvarmatrix.nrow!=0 && invvarmatrix.ncol!=0)
> > + {
> > + tX = tX*invvarmatrix;
> > + }
> > + /*
> > + fprintf(stdout,"\n");
> > + fprintf(stdout,"X %f %f %f\n",X.get(0,0),X.get(0,1),X.get(0,2));
> > + if (X.ncol==4) fprintf(stdout,"X[4] %f\n",X.get(0,3));
> > + fprintf(stdout,"Inv %f %f %f
> > \n",invvarmatrix.get(0,0),invvarmatrix.get(0,1),invvarmatrix.get(0,2));
> > + if (X.ncol==4) fprintf(stdout,"X[4] %f\n",invvarmatrix.get(0,3));
> > + fprintf(stdout,"tXInv %f %f %f
> > \n",tX.get(0,0),tX.get(1,0),tX.get(2,0));
> > + if (X.ncol==4) fprintf(stdout,"X[4] %f\n",tX.get(3,0));
> > + */
> > 
> > -
> > -
> > double N;
> > 
> > niter=0;
> > @@ -700,21 +736,29 @@
> > N = tXWX.get(0,0);
> > 
> > if (verbose) {printf("tXWX:\n");tXWX.print();}
> > + //printf("tXWX:\n");tXWX.print();
> > //
> > // use cholesky to invert
> > //
> > tXWX_i = tXWX;
> > - cholesky2_mm(tXWX_i,tol_chol);
> > - if (verbose) {printf("chole tXWX:\n");tXWX_i.print();}
> > - chinv2_mm(tXWX_i);
> > + //cholesky2_mm(tXWX_i,tol_chol);
> > + //if (verbose) {printf("chole tXWX:\n");tXWX_i.print();}
> > + //printf("chole tXWX:\n");tXWX_i.print();
> > + //chinv2_mm(tXWX_i);
> > // was before
> > - // tXWX_i=invert(tXWX);
> > + tXWX_i=invert(tXWX);
> > if (verbose) {printf("tXWX-1:\n");tXWX_i.print();}
> > + //fprintf(stdout,"*** tXWX_i\n");tXWX_i.print();
> > mematrix<double> tmp1 = productMatrDiag(tX,W);
> > mematrix<double> tXWz = tmp1*z;
> > if (verbose) {printf("tXWz:\n");tXWz.print();}
> > beta = tXWX_i*tXWz;
> > + //fprintf(stdout,"*** res: %f %f %f
> > \n",residuals[0],residuals[1],residuals[2]);
> > + //mematrix<double> txres = tx * residuals;
> > + //fprintf(stdout,"*** txres\n");txres.print();
> > + //beta = txwx_i* txres;
> > if (verbose) {printf("beta:\n");beta.print();}
> > + //printf("beta:\n");beta.print();
> > // compute likelihood
> > prevlik = loglik;
> > loglik=0.;
> > @@ -780,6 +824,9 @@
> > }
> > }
> > if (verbose) {printf("sebeta (%d):\n",sebeta.nrow);sebeta.print();}
> > + //printf("sebeta (%d):\n",beta.nrow);beta.print();
> > + //printf("sebeta (%d):\n",sebeta.nrow);sebeta.print();
> > + //exit(1);
> > }
> > // just a stupid copy from linear_reg
> > void score(mematrix<double> &resid,regdata &rdata,int verbose,
> > double tol_chol, int model, int interaction, int ngpreds,
> > mematrix<double> & invvarmatrix, int nullmodel=0)
> > 
> > Modified: pkg/ProbABEL/src/usage.h
> > ===================================================================
> > --- pkg/ProbABEL/src/usage.h 2011-08-22 08:32:43 UTC (rev 761)
> > +++ pkg/ProbABEL/src/usage.h 2011-08-23 19:48:36 UTC (rev 762)
> > @@ -22,7 +22,7 @@
> > fprintf(stdout,"\t --allcov  : report estimates for all covariates
> > (large outputs!)\n");
> > fprintf(stdout,"\t --interaction: Which covariate to use for
> > interaction with SNP analysys (default is no ineraction, 0)\n");
> > fprintf(stdout,"\t --interaction_only: like previos but without
> > covariate acting in interaction with SNP (default is no ineraction,
> > 0)\n");
> > - fprintf(stdout,"\t --mmscore : score test in samples of related
> > individuals. File with inverse of variance-covariance matrix as
> > input parameter\n");
> > + fprintf(stdout,"\t --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
> > \n");
> > fprintf(stdout,"\t --robust  : report robust (aka sandwich, aka
> > Hubert-White) standard errors\n");
> > fprintf(stdout,"\t --help    : print help\n");
> > exit(exit_code);
> > 
> > _______________________________________________
> > Genabel-commits mailing list
> > Genabel-commits at lists.r-forge.r-project.org
> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
> > 
> 
> 
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-- 
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L.C. Karssen
Erasmus MC
Department of Epidemiology
Room 2224

Postbus 2040
3000 CA Rotterdam
The Netherlands

phone: +31-10-7044217
fax: +31-10-7044657
e-mail: l.karssen at erasmusmc.nl
GPG key ID: 0E1D39E3
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