[Genabel-commits] r1751 - in branches/ProbABEL-v0.4.3-coxfix/ProbABEL: . src

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2014-06-10 14:49:25 +0200 (Tue, 10 Jun 2014)
New Revision: 1751

Modified:
   branches/ProbABEL-v0.4.3-coxfix/ProbABEL/configure.ac
   branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/coxph_data.cpp
   branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/main.cpp
Log:
In the ProbABEL v0.4.3 coxfix branch: Added some debug print statements and decrease EPS to the same value as used by R trying to find the cause of the Cox problems.


Modified: branches/ProbABEL-v0.4.3-coxfix/ProbABEL/configure.ac
===================================================================
--- branches/ProbABEL-v0.4.3-coxfix/ProbABEL/configure.ac	2014-05-29 13:23:32 UTC (rev 1750)
+++ branches/ProbABEL-v0.4.3-coxfix/ProbABEL/configure.ac	2014-06-10 12:49:25 UTC (rev 1751)
@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.67])
-AC_INIT(ProbABEL, 0.4.3-coxfix1, genabel-devel at r-forge.wu-wien.ac.at)
+AC_INIT(ProbABEL, 0.4.3-coxfix2, genabel-devel at r-forge.wu-wien.ac.at)
 AM_INIT_AUTOMAKE([silent-rules subdir-objects])
 AM_SILENT_RULES([yes])
 AC_CONFIG_SRCDIR([src/data.h])

Modified: branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/coxph_data.cpp
===================================================================
--- branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/coxph_data.cpp	2014-05-29 13:23:32 UTC (rev 1750)
+++ branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/coxph_data.cpp	2014-06-10 12:49:25 UTC (rev 1751)
@@ -438,6 +438,17 @@
 
     niter = maxiter;
 
+    cerr << snpinfo.name[cursnp]
+         << ": MAF = " << snpinfo.MAF[cursnp]
+         << "; Freq1 = " << snpinfo.Freq1[cursnp]
+         << "; Rsq = " << snpinfo.Rsq[cursnp]
+         << "; FLAG = " << flag
+         << "; niter = " << maxiter
+         << "; imat.nrow = " << imat.data.rows()
+         << "; X.nrow = " << X.nrow
+         << "; X.ncol = " << X.ncol
+         << "\n";
+
     // Check the results of the Cox fit; mirrored from the same checks
     // in coxph.fit.S and coxph.R from the R survival package.
 
@@ -452,6 +463,7 @@
         cerr << "Warning for " << snpinfo.name[cursnp]
              << ": X matrix deemed to be singular,"
              << " setting beta and se to 'NaN'\n";
+
         setToNAN = true;
     }
 
@@ -493,11 +505,11 @@
                  << ": beta may be infinite,"
                  << " setting beta and se to 'NaN'\n";
 
-            // cout << "beta values for SNP: " << snpinfo.name[cursnp]
-            //      << " are: " << betaeigen << std::endl;
-
             setToNAN = true;
         }
+
+        // cout << "beta values for SNP: " << snpinfo.name[cursnp]
+        //      << " are: " << betaeigen << std::endl;
 #else
         cerr << "Warning for " << snpinfo.name[cursnp]
              << ": can't check for infinite betas."

Modified: branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/main.cpp
===================================================================
--- branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/main.cpp	2014-05-29 13:23:32 UTC (rev 1750)
+++ branches/ProbABEL-v0.4.3-coxfix/ProbABEL/src/main.cpp	2014-06-10 12:49:25 UTC (rev 1751)
@@ -83,7 +83,7 @@
 /// Maximum number of iterations we allow the regression to run
 #define MAXITER 20
 /// Tolerance for convergence
-#define EPS 1.e-8
+#define EPS 1.e-9
 /// Precision for the Cholesky decomposition
 #define CHOLTOL 1.5e-12