string getOutputPattern(string);
string getHelpString();
- string getCitation() { return "http://www.mothur.org/wiki/Lefse"; }
+ string getCitation() { return "Segata, N., J. Izard, L. Waldron, D. Gevers, L. Miropolsky, W. S. Garrett, and C. Huttenhower. 2011. Metagenomic biomarker discovery and explanation. Genome Biol 12:R60, http://www.mothur.org/wiki/Lefse"; }
string getDescription() { return "brief description"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
- bool abort, allLines;
- string outputDir, sharedfile, designfile, mclass, subclass, classes;
+ bool abort, allLines, wilc, wilcsamename, curv, subject, normMillion;
+ string outputDir, sharedfile, designfile, mclass, subclass, rankTec, multiClassStrat;
vector<string> outputNames;
set<string> labels;
- float anovaAlpha, wilcoxonAlpha;
+ double anovaAlpha, wilcoxonAlpha, fBoots, ldaThreshold;
+ int nlogs, iters, strict, minC;
- int process(vector<SharedRAbundVector*>&, DesignMap&);
- vector<int> runKruskalWallis(vector<SharedRAbundVector*>&, DesignMap&);
- vector<int> runWilcoxon(vector<SharedRAbundVector*>&, DesignMap&, vector<int>);
-
+ int process(vector<SharedRAbundFloatVector*>&, DesignMap&);
+ int normalize(vector<SharedRAbundFloatVector*>&);
+ map<int, double> runKruskalWallis(vector<SharedRAbundFloatVector*>&, DesignMap&);
+ map<int, double> runWilcoxon(vector<SharedRAbundFloatVector*>&, DesignMap&, map<int, double>, map<string, set<string> >& class2SubClasses, map<string, vector<int> >& subClass2GroupIndex, map<string, string>);
+ bool testOTUWilcoxon(map<string, set<string> >& class2SubClasses, vector<float> abunds, map<string, vector<int> >& subClass2GroupIndex, map<string, string>);
+ map<int, double> testLDA(vector<SharedRAbundFloatVector*>&, map<int, double>, map<string, vector<int> >& class2GroupIndex, map<string, vector<int> >&);
+ bool contastWithinClassesOrFewPerClass(vector< vector<double> >&, vector<int> rands, int minCl, map<string, vector<int> > class2GroupIndex, map<int, string> indexToClass);
+ vector< vector<double> > lda(vector< vector<double> >& adjustedLookup, vector<int> rand_s, map<int, string>& indexToClass, vector<string>);
+ vector< vector<double> > getMeans(vector<SharedRAbundFloatVector*>& lookup, map<string, vector<int> >& class2GroupIndex);
+ int printResults(vector< vector<double> >, map<int, double>, map<int, double>, string, vector<string>);
+
+ //for testing
+ bool printToCoutForRTesting(vector< vector<double> >& adjustedLookup, vector<int> rand_s, map<string, vector<int> >& class2GroupIndex, map<int, double> bins, map<string, vector<int> >&, vector<string>);
+ int makeShared(int);
};
/**************************************************************************************************/