[Genabel-commits] r757 - in pkg/VariABEL/src: ITERlib VARlib

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

Author: maksim
Date: 2011-07-28 12:29:42 +0200 (Thu, 28 Jul 2011)
New Revision: 757

Modified:
   pkg/VariABEL/src/ITERlib/iterator_functions.cpp
   pkg/VariABEL/src/VARlib/supplementary_functions.cpp
   pkg/VariABEL/src/VARlib/var_homogeneity_test_C.cpp
   pkg/VariABEL/src/VARlib/var_homogeneity_tests.cpp
Log:
fix leven's test. genotypic groups were detemined wrongly

Modified: pkg/VariABEL/src/ITERlib/iterator_functions.cpp
===================================================================
--- pkg/VariABEL/src/ITERlib/iterator_functions.cpp	2011-07-27 13:38:09 UTC (rev 756)
+++ pkg/VariABEL/src/ITERlib/iterator_functions.cpp	2011-07-28 10:29:42 UTC (rev 757)
@@ -473,9 +473,9 @@
 	double *trait = new double[indataHeight];	
 
 
-	for(int i=0 ; i<indataHeight*(*p) ; i++) design_matrix[i] = design_matrix_[i];
-	for(int i=0 ; i<indataHeight*(*p) ; i++) design_matrix_copy[i] = design_matrix_copy_[i];
-	for(int i=0 ; i<indataHeight ; i++) trait[i] = trait_[i];
+	for(unsigned i=0 ; i<indataHeight*(*p) ; i++) design_matrix[i] = design_matrix_[i];
+	for(unsigned i=0 ; i<indataHeight*(*p) ; i++) design_matrix_copy[i] = design_matrix_copy_[i];
+	for(unsigned i=0 ; i<indataHeight ; i++) trait[i] = trait_[i];
 
 	//indataHeight is nids;
 
@@ -489,7 +489,7 @@
 		is_trait_na[id_counter]=0;
 		
 		//NA among covariates
-		for(unsigned column_counter=0 ; column_counter<*p ; column_counter++)
+		for(int column_counter=0 ; column_counter<*p ; column_counter++)
 			{
 			if(ISNAN(design_matrix[id_counter + column_counter*indataHeight])) {is_trait_na[id_counter]=1;}
 			}

Modified: pkg/VariABEL/src/VARlib/supplementary_functions.cpp
===================================================================
--- pkg/VariABEL/src/VARlib/supplementary_functions.cpp	2011-07-27 13:38:09 UTC (rev 756)
+++ pkg/VariABEL/src/VARlib/supplementary_functions.cpp	2011-07-28 10:29:42 UTC (rev 757)
@@ -882,32 +882,34 @@
 	if(snp[id]>1.5 && snp[id]<=2. ) snp_value=2;
 	//________________		
 
+//	std::cout<<"id="<<id<<", snp_value="<<snp_value<<"\n";
+
 		//spread ids trait among genotype group
 		switch(snp_value)
 			{
+//			case 0:
+//				{
+//				//NA.push_back(trait[id]);
+//				}
+			break;
 			case 0:
 				{
-				//NA.push_back(trait[id]);
+				AA.push_back(trait[id]);
 				}
 			break;
 			case 1:
 				{
-				AA.push_back(trait[id]);
+				AB.push_back(trait[id]);
 				}
 			break;
 			case 2:
 				{
-				AB.push_back(trait[id]);
-				}
-			break;
-			case 3:
-				{
 				BB.push_back(trait[id]);
 				}
 			break;
 			default:
 				{
-				Rprintf("error: VarABEL: Unexpected genotype code has been detected (%i, %i). Only 0, 1, 2, 3, NA are alowed\n", &snp[id], snp[id]);
+				Rprintf("error: VarABEL: Unexpected genotype code has been detected (%i, %i). Only 0, 1, 2, NA are alowed\n", &snp[id], snp[id]);
 				return;	
 				}
 			break;

Modified: pkg/VariABEL/src/VARlib/var_homogeneity_test_C.cpp
===================================================================
--- pkg/VariABEL/src/VARlib/var_homogeneity_test_C.cpp	2011-07-27 13:38:09 UTC (rev 756)
+++ pkg/VariABEL/src/VARlib/var_homogeneity_test_C.cpp	2011-07-28 10:29:42 UTC (rev 757)
@@ -68,12 +68,12 @@
 
 void variance_homogeneity_test_C(double* snp, double *trait, double *design_matrix_copy, double *design_matrix, int *p_, long unsigned* nids_, double *betas, double *se, double * chi2, int * df, double * residuals, int *analys_type_, int * is_trait_na, int *testname, /*auxiliary variables:*/ double *qty, int *jpvt, double *qraux, double *work, double *v, double *x_for_ch2inv)
 {
-//std::cout<<"variance_homogeneity_test_C: START\n";
 		
 std::list<my_small_vector> trait_groups;
 static chisq_df chisq;
 
 
+
 if(*testname != sqlm)
 	{
 	break_trait_up_into_groups(&trait_groups, snp, trait, nids_, *analys_type_, is_trait_na); 

Modified: pkg/VariABEL/src/VARlib/var_homogeneity_tests.cpp
===================================================================
--- pkg/VariABEL/src/VARlib/var_homogeneity_tests.cpp	2011-07-27 13:38:09 UTC (rev 756)
+++ pkg/VariABEL/src/VARlib/var_homogeneity_tests.cpp	2011-07-28 10:29:42 UTC (rev 757)
@@ -183,6 +183,7 @@
   if(snp->COUNTS[i] == 0 || is_na(snp->COUNTS[i])) continue;
 	common_mean += snp->MEAN[i]*snp->COUNTS[i];
 	N += snp->COUNTS[i];
+	std::cout<<"snp->COUNTS["<<i<<"]="<<snp->COUNTS[i]<<"\n";
 	geno_group_num++;
 	}
 
@@ -216,6 +217,7 @@
 
 chisq = (N-geno_group_num)*var_mean/(var_sum*df);
 
+std::cout<<"leven_test: chisq="<<chisq<<", df="<<df<<"\n";
 
 return chisq_df(chisq, df);