[Genabel-commits] r1023 - branches/ProbABEL-refactoring/ProbABEL/src

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

Author: lckarssen
Date: 2012-11-15 10:05:12 +0100 (Thu, 15 Nov 2012)
New Revision: 1023

Modified:
   branches/ProbABEL-refactoring/ProbABEL/src/coxph_data.cpp
   branches/ProbABEL-refactoring/ProbABEL/src/phedata.h
   branches/ProbABEL-refactoring/ProbABEL/src/regdata.cpp
Log:
Ported the changes of r910 and r933 from trunk to the ProbABEL-refactoring branch. 
These were the original SVN log messages:

r933:
Added copyright message for the Nijmegen bug fix also to the current branch.

r910:
ProbABEL:
"Forward port" of the fix from rev. 902 in the ProbABEL-pacoxph branch where the behaviour for pacoxph was fixed for .prob files (ngpreds=2).

WARNING: NOT WELL TESTED YET BECAUSE pacoxph STILL RUNS VERY SLOW SINCE THE ADDITION OF FILEVECTOR STUFF.



Modified: branches/ProbABEL-refactoring/ProbABEL/src/coxph_data.cpp
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/src/coxph_data.cpp	2012-11-15 07:45:09 UTC (rev 1022)
+++ branches/ProbABEL-refactoring/ProbABEL/src/coxph_data.cpp	2012-11-15 09:05:12 UTC (rev 1023)
@@ -92,12 +92,12 @@
         sstat[i] = int((phed.Y).get(i, 1));
         if (sstat[i] != 1 && sstat[i] != 0)
         {
-            fprintf(stderr,
-                    "coxph_data: status not 0/1 (right order: id, fuptime, status ...) %d \n",
-                    phed.noutcomes);
+	  std::cerr << "coxph_data: status not 0/1 (correct order: id, fuptime, status ...)"
+		    << endl;
             exit(1);
         }
     }
+
     for (int j = 0; j < phed.ncov; j++)
         for (int i = 0; i < nids; i++)
             X.put((phed.X).get(i, j), i, j);
@@ -163,25 +163,37 @@
 }
 void coxph_data::update_snp(gendata &gend, int snpnum)
 {
-    // note this sorts by "order"!!!
+  /**
+   * This is the main part of the fix of bug #1846
+   * (C) of the fix:
+   *   UMC St Radboud Nijmegen,
+   *   Dept of Epidemiology & Biostatistics,
+   *   led by Prof. B. Kiemeney
+   *
+   * Note this sorts by "order"!!!
+   * Here we deal with transposed X, hence last two arguments are swapped
+   * compared to the other 'update_snp'
+   * Also, the starting column-1 is not necessary for cox X therefore
+   * 'ncov-j' changes to 'ncov-j-1'
+   **/
 
     for (int j = 0; j < ngpreds; j++)
     {
         float snpdata[nids];
         for (int i = 0; i < nids; i++)
             masked_data[i] = 0;
+
         gend.get_var(snpnum * ngpreds + j, snpdata);
+
         for (int i = 0; i < nids; i++)
         {
-            X.put(snpdata[i], (ncov - ngpreds + j), order[i]);
+            X.put(snpdata[i], (ncov - j - 1), order[i]);
             if (isnan(snpdata[i]))
                 masked_data[order[i]] = 1;
         }
     }
-    //      for (int i=0;i<nids;i++)
-    //          for (int j=0;j<ngpreds;j++)
-    //              X.put((gend.G).get(i,(snpnum*ngpreds+j)),(ncov-ngpreds+j),order[i]);
 }
+
 coxph_data::~coxph_data()
 {
     delete[] coxph_data::masked_data;

Modified: branches/ProbABEL-refactoring/ProbABEL/src/phedata.h
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/src/phedata.h	2012-11-15 07:45:09 UTC (rev 1022)
+++ branches/ProbABEL-refactoring/ProbABEL/src/phedata.h	2012-11-15 09:05:12 UTC (rev 1023)
@@ -43,8 +43,8 @@
     int noutcomes;
     int ncov;
     unsigned short int * allmeasured;
-    mematrix<double> X;
-    mematrix<double> Y;
+    mematrix<double> X;       /* Will contain the values of the covariate(s) */
+    mematrix<double> Y;       /* Will contain the values of the outcome(s) */
     std::string * idnames;
     std::string model;
     std::string * model_terms;

Modified: branches/ProbABEL-refactoring/ProbABEL/src/regdata.cpp
===================================================================
--- branches/ProbABEL-refactoring/ProbABEL/src/regdata.cpp	2012-11-15 07:45:09 UTC (rev 1022)
+++ branches/ProbABEL-refactoring/ProbABEL/src/regdata.cpp	2012-11-15 09:05:12 UTC (rev 1023)
@@ -95,10 +95,12 @@
         float snpdata[nids];
         for (int i = 0; i < nids; i++)
             masked_data[i] = 0;
+
         gend.get_var(snpnum * ngpreds + j, snpdata);
+
         for (int i = 0; i < nids; i++)
         {
-            X.put(snpdata[i], i, (ncov + 1 - j - 1));
+            X.put(snpdata[i], i, (ncov - j));
             if (isnan(snpdata[i]))
                 masked_data[i] = 1;
         }