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//
// sparcccommand.h
// Mothur
//
// Created by SarahsWork on 5/10/13.
// Copyright (c) 2013 Schloss Lab. All rights reserved.
//
#ifndef Mothur_sparcccommand_h
#define Mothur_sparcccommand_h
#include "command.hpp"
#include "inputdata.h"
#include "calcsparcc.h"
/**************************************************************************************************/
class SparccCommand : public Command {
public:
SparccCommand(string);
~SparccCommand(){}
vector<string> setParameters();
string getCommandName() { return "sparcc"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getOutputPattern(string);
//commmand category choices: Sequence Processing, OTU-Based Approaches, Hypothesis Testing, Phylotype Analysis, General, Clustering and Hidden
string getHelpString();
string getCitation() { return "Friedman J, Alm EJ (2012) Inferring Correlation Networks from Genomic Survey Data. PLoS Comput Biol 8(9): e1002687. doi:10.1371/journal.pcbi.1002687 http://www.mothur.org/wiki/Sparcc"; }
string getDescription() { return "Calculates correlations between OTUs using a method that is insensitive to the use of relative abundance data"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, allLines;
string sharedfile, normalizeMethod;
int numSamplings, maxIterations, numPermutations, processors;
set<string> labels;
vector<string> Groups;
vector<string> outputNames;
int process(SharedRAbundVectors*&);
vector<vector<float> > createProcesses(vector<vector<float> >&, vector<vector<float> >&);
//vector<vector<float> > driver(vector<vector<float> >&, vector<vector<float> >&, int);
//vector<vector<float> > shuffleSharedVector(vector<vector<float> >&);
};
/**************************************************************************************************/
#endif
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