/
enrich.h
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/
enrich.h
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//////////////////////////////////////////////////////////////////////
// GOUtil.h Copyright (c) 2017 Dario Ghersi //
// Version: 20171211 //
// //
// This file is part of the GOUtil suite. //
// GOUtil is free software: you can redistribute it and/or //
// modify it under the terms of the GNU General Public License as //
// published by the Free Software Foundation, either version 3 of //
// the License, or (at your option) any later version. //
// //
// GOUtil is distributed in the hope that it will be useful, //
// but WITHOUT ANY WARRANTY; without even the implied warranty of //
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the //
// GNU General Public License for more details. //
// //
// You should have received a copy of the GNU General Public //
// License along with GOUtil. //
// If not, see <http://www.gnu.org/licenses/>. //
//////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////
// CONSTANTS //
//////////////////////////////////////////////////////////////////////
const string USAGE = "\nUsage:\nGOUtil -e EDGE_LIST -a ANNOTATIONS -b BACKGROUND -t TARGET -o OUTFILE -p FDR_THRESHOLD\n";
//////////////////////////////////////////////////////////////////////
// CLASSES, STRUCTS, AND TYPEDEFS //
//////////////////////////////////////////////////////////////////////
class EnrichedTerms {
public:
vector<unsigned int> termIndex;
vector<string> termID;
vector<string> definition;
vector<double> pvalues;
vector<double> adjustedP;
vector<double> enrichFactor;
vector<unsigned int> sortedOrder;
unordered_map<unsigned int, set<string> > withTerm;
void addID(unordered_map<unsigned int, string>);
void fdrCorrection();
void printResults(string, double,
unordered_map<unsigned int, string> &);
};
//////////////////////////////////////////////////////////////////////
class Parameters {
public:
char *edgesFileName;
string annotationsFileName;
string backgroundSetFileName;
string targetSetFileName;
string outFileName;
double threshold;
Parameters(char **, int);
};
typedef pair<unsigned int, double> intDouble;
//////////////////////////////////////////////////////////////////////
// PROTOTYPES //
//////////////////////////////////////////////////////////////////////
void calculateBackgroundFreq(vector<unsigned int> &,
vector<unsigned int> &,
vector<vector<string> >,
vector<vector<string> >,
Graph,
unordered_map<unsigned int, set<string> > &);
bool cmdOptionExists(char **, char **, const string &);
char *getCmdOption(char **, char **, const string &);
void doEnrichment(unsigned int, unsigned int, Graph,
vector<vector<string> >, vector<vector<string> >,
EnrichedTerms &);
void findAllAncestors(set<unsigned int> &, set<unsigned int> &, Graph &);
void storeSet(set<string> &, string);
void storeTermCentricAnn(set<string> &,
vector<vector<string> > &,
vector<vector<string> > &, string,
unordered_map<string, unsigned int>,
set<string> &);