Changeset 1304 for trunk

Timestamp:

May 14, 2008, 10:11:57 PM (13 years ago)

Author:

Peter

Message:

quantile normalization closes #288

Location:

trunk

Files:

• test/Suite.cc (modified) (1 diff)
• test/Suite.h (modified) (1 diff)
• test/utility_test.cc (modified) (3 diffs)
• yat/utility/utility.cc (modified) (2 diffs)
• yat/utility/utility.h (modified) (2 diffs)

trunk/test/Suite.cc

@@ -62 +62 @@
 
 
-  void Suite::add(bool ok)
+  bool Suite::add(bool ok)
   {
     ok_ = ok_ && ok;
+    return ok;
   }
 

trunk/test/Suite.h

@@ -45 +45 @@
     /**
        set ok to 'b && ok' 
+
+       \return b
     */
-    void add(bool b);
+    bool add(bool b);
 
     /**

trunk/test/utility_test.cc

@@ -26 +26 @@
 #include "Suite.h"
 
+#include "yat/utility/Matrix.h"
 #include "yat/utility/utility.h"
 #include "yat/utility/stl_utility.h"
@@ -32 +33 @@
 #include <iostream>
 #include <string>
+
+using namespace theplu::yat;
+void test_quantile_normalize(test::Suite&);
 
 int main(int argc, char* argv[])
@@ -113 +117 @@
   }
 
+  test_quantile_normalize(suite);
+
   return suite.return_value();
 }
+
+void test_quantile_normalize(test::Suite& suite)
+{
+  suite.err() << "Testing quantile normalization\n";
+  
+  utility::Matrix m(2,2);
+  m(0,0) = 0;
+  m(0,1) = 10;
+  m(1,0) = 2;
+  m(1,1) = 4;
+  utility::quantile_normalize(m);
+  suite.err() << "Testing m(0,0)\n";
+  suite.add(suite.equal(m(0,0), 2));
+  suite.err() << "Testing m(0,1)\n";
+  suite.add(suite.equal(m(0,1), 6));
+  suite.err() << "Testing m(1,0)\n";
+  suite.add(suite.equal(m(1,0), 6));
+  suite.err() << "Testing m(1,1)\n";
+  suite.add(suite.equal(m(1,1), 2));
+
+}

trunk/yat/utility/utility.cc

@@ -25 +25 @@
 #include "utility.h"
 
+#include "Matrix.h"
 #include "stl_utility.h"
+#include "VectorConstView.h"
+#include "yat/statistics/Averager.h"
 
 #include <sstream>
@@ -102 +105 @@
 
 
+  void quantile_normalize(Matrix& data)
+  {
+    Matrix data_copy(data);
+    
+    // sort columns in copy
+    for (size_t column=0; column<data_copy.columns(); ++column){
+      std::sort(data_copy.begin_column(column), data_copy.end_column(column));
+    }
+
+    // calculate average of each row
+    std::vector<yat::statistics::Averager> averager(data_copy.rows());
+    for (size_t row=0; row<data_copy.rows(); ++row){
+      add(averager[row], data_copy.begin_row(row), data_copy.end_row(row));
+    }
+
+    for (size_t column=0; column<data.columns(); ++column){
+      std::vector<size_t> index;
+      const VectorConstView col_vec(data,column,false);
+      yat::utility::sort_index(index, data.column_const_view(column));
+                               
+      for (size_t row=0; row<data.rows(); ++row)
+        data(index[row], column) = averager[row].mean();
+    }
+  }
+
+
 
 }}} // end of namespace utility, yat and thep

trunk/yat/utility/utility.h

@@ -44 +44 @@
 namespace utility {
 
-  class vector;
+  class Matrix;
 
   /**
@@ -81 +81 @@
   bool is_nan(const std::string& s);
 
+  /**
+     \brief Perform quantile normalization
+   */
+  void quantile_normalize(Matrix&);
 
   // template implementations