BioInt  1.02.00
BioInt: An integrative biological object-oriented application framework and interpreter
BioDataSet.h
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00001 #ifndef BIODATASET_H
00002 #define BIODATASET_H
00003 
00004 
00005 #include "BioUtilities.h"
00006 #include "BioStatistics.h"
00007 #include "BioProbeSet.h"
00008 #include "BioSampleSet.h"
00009 
00010 class BioDataSet
00011 {
00012 protected:
00013         BioDataSet(); // Default Constructor - NOT TO BE USED, hence PRIVATE;
00014         vector<BioProbeSet> probeData_;
00015         vector<string>sampleNames_;
00016 public:
00017 
00018         BioDataSet(vector<string>&  sampleNames, vector<BioProbeSet>& prbData);
00019         BioProbeSet getProbeSet(int probeIndex);
00020 
00021         BioProbeSet getAverageOfProbeSets(string probeIndexPattern);
00022 
00023         int getNumberOfSamples();
00024 
00025         int getNumberOfProbes();
00026 
00027         int getSampleIndex(string sampleName);
00028 
00029         int getProbeIndex(string probeReference);
00030 
00031         BioSampleSet getSampleSet(int sampleIndex);
00032 
00033         BioSampleSet getAverageOfSampleSets( string sampleIndexPattern);
00034 
00035         BioDataSet getMultipleProbeSets(string indexString);
00036 
00037         BioDataSet getMultipleSampleSets(string indexString);
00038 
00039         float getSampleRMSD( int sampleIndex1, int sampleIndex2);
00040 
00041         float getProbeRMSD( int probeIndex1, int probeIndex2);
00042 
00043         float getProbeCorrelationCoefficient( int probeIndex1, int probeIndex2);
00044 
00045         float getSampleCorrelationCoefficient( int sampleIndex1, int sampleIndex2);
00046 
00047         vector<int> getProbeIndexListExcludingAllNullProbes();
00048         vector<int> getControlProbeIndexList();
00049         vector<int> getAllNullProbeIndexList();
00050         vector<int> getCleanProbeIndexList();
00051         vector<int> getAllNullSampleIndexList();
00052         vector<int> getCleanSampleIndexList();
00053 
00054         BioDataSet getNormalizedDataSet();
00055         float getMean();
00056         float getMaximum();
00057         float getMinimum();
00058         float getStandardDeviation();
00059         float getMedian();
00060         
00061         BioDataSet getCleanDataSet();
00062         BioDataSet getDataSetExcludingControlProbes();
00063         
00064 };
00065 
00066 #endif
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