/*
* #%L
* org.gitools.analysis
* %%
* Copyright (C) 2013 - 2014 Universitat Pompeu Fabra - Biomedical Genomics group
* %%
* This program 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.
*
* This program 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 this program. If not, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
package org.gitools.analysis.enrichment;
import junit.framework.Assert;
import org.gitools.analysis.AbstractProcessorTest;
import org.gitools.analysis.AnalysisException;
import org.gitools.analysis.AnalysisProcessor;
import org.gitools.analysis.AssertMatrix;
import org.gitools.analysis.htest.enrichment.EnrichmentAnalysis;
import org.gitools.analysis.htest.enrichment.EnrichmentProcessor;
import org.gitools.api.matrix.IMatrix;
import org.gitools.api.matrix.MatrixDimensionKey;
import org.junit.Test;
import java.io.IOException;
import static junit.framework.Assert.assertEquals;
import static org.gitools.api.ApplicationContext.getProgressMonitor;
public class ZScoreEnrichmentProcessorTest extends AbstractProcessorTest<EnrichmentAnalysis> {
public ZScoreEnrichmentProcessorTest() {
super(EnrichmentAnalysis.class, "/enrichment/test02.enrichment");
}
@Test
public void testAnalysisProcessor() throws IOException {
EnrichmentAnalysis analysis = getAnalysis();
// Keep the correct results
IMatrix resultsOk = analysis.getResults().get();
analysis.setResults(null);
// Execute the analysis
try {
AnalysisProcessor processor = new EnrichmentProcessor(analysis);
processor.run(getProgressMonitor());
} catch (AnalysisException e) {
e.printStackTrace();
}
// Test the store and load
IMatrix results = storeAndLoadMatrix(analysis.getResults().get());
// Compare the two matrices
for (MatrixDimensionKey key : resultsOk.getDimensionKeys()) {
assertEquals(resultsOk.getDimension(key), results.getDimension(key));
}
Assert.assertEquals(resultsOk.getLayers().size(), results.getLayers().size());
AssertMatrix.assertEquals("N", resultsOk, results);
AssertMatrix.assertEquals("observed", resultsOk, results);
AssertMatrix.assertEquals("expected-mean", resultsOk, results, 0.004);
AssertMatrix.assertEquals("expected-stdev", resultsOk, results, 0.03);
AssertMatrix.assertEquals("z-score", resultsOk, results, 0.7);
AssertMatrix.assertEquals("left-p-value", resultsOk, results, 0.07);
AssertMatrix.assertEquals("right-p-value", resultsOk, results, 0.07);
AssertMatrix.assertEquals("two-tail-p-value", resultsOk, results, 0.13);
AssertMatrix.assertEquals("corrected-left-p-value", resultsOk, results, 0.48);
AssertMatrix.assertEquals("corrected-right-p-value", resultsOk, results, 0.48);
AssertMatrix.assertEquals("corrected-two-tail-p-value", resultsOk, results, 0.68);
}
}