Implementing new method to FET computing, not in used actually

cpp/utils.cpp

@@ -214,3 +214,109 @@ char checkBase(char incoming )
 	}
 	return 'N';
 }
+
+
+
+//Method for calculating a sd from a vector of double
+double sd_calculator( vector<double> incVector )
+{
+	// Déclarations
+	double sd;
+	double temp_value;
+	double sumone = 0;
+	double sumtwo = 0;
+	double moyenne;
+	int number = 0;
+	double variance;
+
+	// calcul des moyennes et moyennes carrées
+	vector<double>::iterator myIter;
+	for( myIter = incVector.begin() ; myIter != incVector.end() ; myIter ++ )
+	{
+		temp_value = * myIter;
+
+		sumone += temp_value;
+		sumtwo += ( temp_value * temp_value );
+		number ++;
+	}
+
+	// calcul de la moyenne
+	moyenne = sumone / number;
+	// Calcul de la variance
+	variance = ( sumtwo / number ) - ( moyenne * moyenne );
+	// Calcul ecart type
+	sd = sqrt(variance);
+
+	return sd;
+}
+
+// Method for calculating a mean from a vector of double
+double moyenne_calculator( vector<double> incVector )
+{
+	// Déclarations
+	double temp_value;
+	double sumone;
+	double moyenne;
+	int number = 0;
+
+	// calcul des moyennes et moyennes carrées
+	vector<double>::iterator myIter;
+	for( myIter = incVector.begin() ; myIter != incVector.end() ; myIter ++ )
+	{
+		temp_value = * myIter;
+		sumone += temp_value;
+		number ++;
+	}
+
+	// calcul de la moyenne
+	if( number != 0 )
+	{
+		moyenne = sumone / number;
+	}
+	else
+	{
+		return 0;
+	}
+	return moyenne;
+}
+
+// Method for calculating fisher exact test 2-sided, return the pvalue.
+double FET( int a , int b , int c , int d )
+{
+	int n = a + b + c + d;
+	double logpCutOff = logHypergeometricProb( a , b , c , d );
+	double pFraction = 0;
+	double logpValue = 0;
+
+	for( int x = 0 ; x <= n ; x ++ )
+	{
+		if( ( a + b - x >= 0 ) && ( a + c - x >= 0 ) && ( d - a + x >= 0 ) )
+		{
+			double l = logHypergeometricProb( x , a + b - x , a + c - x , d - a + x );
+			if( l <= logpCutOff )
+			{
+				pFraction += exp( l - logpCutOff );
+			}
+		}
+	}
+	logpValue = logpCutOff + log( pFraction );
+
+	return exp(logpValue);
+}
+
+// method for calculating the hypergeometrical log value  for the FET.
+double logHypergeometricProb( int a , int b , int c  , int d )
+{
+	return logFactoriel( a + b ) + logFactoriel( c + d ) + logFactoriel( a + c ) + logFactoriel( b + d )- logFactoriel( a ) - logFactoriel( b ) - logFactoriel( c ) - logFactoriel( d ) - logFactoriel( a + b + c + d );
+}
+
+// Method for calculating a log factoriel
+double logFactoriel( int inc )
+{
+	double ret;
+	for( ret = 0 ; inc > 0 ; inc -- )
+	{
+		ret += log( (double)inc );
+	}
+	return ret;
+}

cpp/utils.h

@@ -17,7 +17,10 @@ char string_to_char( std::string );
 std::string strip( std::string );
 double chisquare( std::vector<double>, std::vector<double> );
 double fisher_test(std::vector<double> , std::vector<double> );
-
-
+double sd_calculator( std::vector<double> );
+double moyenne_calculator( std::vector<double> );
+double FET( int , int , int , int );
+double logHypergeometricProb( int , int , int , int );
+double logFactoriel( int );
 
 #endif