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Revert "Clenaups for LinearModelAnalyzer"
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gemma-core/src/main/java/ubic/gemma/core/analysis/expression/diff/AbstractAnalyzer.java
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| /* | ||
| * The Gemma project | ||
| * | ||
| * Copyright (c) 2006 University of British Columbia | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| * | ||
| */ | ||
| package ubic.gemma.core.analysis.expression.diff; | ||
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| import org.springframework.beans.factory.annotation.Autowired; | ||
| import ubic.gemma.core.analysis.service.ExpressionDataMatrixService; | ||
| import ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService; | ||
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| /** | ||
| * Analyzer base class. | ||
| * | ||
| * @author keshav | ||
| */ | ||
| public abstract class AbstractAnalyzer { | ||
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| @Autowired | ||
| protected ExpressionDataMatrixService expressionDataMatrixService = null; | ||
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| @Autowired | ||
| protected CompositeSequenceService compositeSequenceService; | ||
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| @SuppressWarnings("unused") // needed for tests. | ||
| public void setExpressionDataMatrixService( ExpressionDataMatrixService expressionDataMatrixService ) { | ||
| this.expressionDataMatrixService = expressionDataMatrixService; | ||
| } | ||
| } |
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...java/ubic/gemma/core/analysis/expression/diff/AbstractDifferentialExpressionAnalyzer.java
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| /* | ||
| * The Gemma project | ||
| * | ||
| * Copyright (c) 2006-2010 University of British Columbia | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| * | ||
| */ | ||
| package ubic.gemma.core.analysis.expression.diff; | ||
|
|
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| import cern.colt.list.DoubleArrayList; | ||
| import cern.colt.matrix.DoubleMatrix1D; | ||
| import org.apache.commons.lang3.ArrayUtils; | ||
| import org.apache.commons.logging.Log; | ||
| import org.apache.commons.logging.LogFactory; | ||
| import ubic.basecode.dataStructure.matrix.DenseDoubleMatrix1D; | ||
| import ubic.basecode.math.MultipleTestCorrection; | ||
| import ubic.basecode.math.Rank; | ||
| import ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix; | ||
| import ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis; | ||
| import ubic.gemma.model.expression.experiment.BioAssaySet; | ||
| import ubic.gemma.model.expression.experiment.ExpressionExperiment; | ||
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| import javax.annotation.Nullable; | ||
| import java.util.Collection; | ||
|
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| /** | ||
| * An abstract differential expression analyzer to be extended | ||
| * | ||
| * @author keshav | ||
| */ | ||
| public abstract class AbstractDifferentialExpressionAnalyzer extends AbstractAnalyzer implements DiffExAnalyzer { | ||
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| private final Log log = LogFactory.getLog( this.getClass() ); | ||
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| @Override | ||
| public abstract Collection<DifferentialExpressionAnalysis> run( ExpressionExperiment expressionExperiment, | ||
| DifferentialExpressionAnalysisConfig config ); | ||
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| @Override | ||
| public abstract Collection<DifferentialExpressionAnalysis> run( ExpressionExperiment expressionExperiment, | ||
| ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config ); | ||
|
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| /** | ||
| * @param pvalues pvalues | ||
| * @return normalized ranks of the pvalues, or null if they were invalid/unusable. | ||
| */ | ||
| double[] computeRanks( double[] pvalues ) { | ||
| if ( pvalues == null ) { | ||
| log.error( "Null pvalues" ); | ||
| return null; | ||
| } | ||
| if ( pvalues.length == 0 ) { | ||
| log.error( "Empty pvalues array" ); | ||
| return null; | ||
| } | ||
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| DoubleArrayList ranks = Rank.rankTransform( new DoubleArrayList( pvalues ) ); | ||
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| if ( ranks == null ) { | ||
| log.error( "Pvalue ranks could not be computed" ); | ||
| return null; | ||
| } | ||
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| double[] normalizedRanks = new double[ranks.size()]; | ||
| for ( int i = 0; i < ranks.size(); i++ ) { | ||
| normalizedRanks[i] = ranks.get( i ) / ranks.size(); | ||
| } | ||
| return normalizedRanks; | ||
| } | ||
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| /** | ||
| * @param pvalues pvalues | ||
| * @return Qvalues, or null if they could not be computed. | ||
| */ | ||
| @Nullable | ||
| double[] benjaminiHochberg( Double[] pvalues ) { | ||
| DoubleMatrix1D benjaminiHochberg = MultipleTestCorrection | ||
| .benjaminiHochberg( new DenseDoubleMatrix1D( ArrayUtils.toPrimitive( pvalues ) ) ); | ||
| return benjaminiHochberg != null ? benjaminiHochberg.toArray() : null; | ||
| } | ||
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| DifferentialExpressionAnalysis initAnalysisEntity( BioAssaySet bioAssaySet, | ||
| DifferentialExpressionAnalysisConfig config ) { | ||
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| if ( config == null ) { | ||
| config = new DifferentialExpressionAnalysisConfig(); | ||
| } | ||
| DifferentialExpressionAnalysis expressionAnalysis = config.toAnalysis(); | ||
| expressionAnalysis.setExperimentAnalyzed( bioAssaySet ); | ||
| return expressionAnalysis; | ||
| } | ||
|
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| /** | ||
| * Needed to convert NaN or infinity values to a value we can store in the database. | ||
| * | ||
| * @param e e | ||
| * @return converted | ||
| */ | ||
| Double nan2Null( Double e ) { | ||
| boolean isNaN = ( e == null || Double.isNaN( e ) || e == Double.NEGATIVE_INFINITY | ||
| || e == Double.POSITIVE_INFINITY ); | ||
| if ( isNaN ) { | ||
| return null; | ||
| } | ||
| return e; | ||
| } | ||
|
|
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| } |
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100 changes: 100 additions & 0 deletions
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gemma-core/src/main/java/ubic/gemma/core/analysis/expression/diff/DiffExAnalyzer.java
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| @@ -0,0 +1,100 @@ | ||
| /* | ||
| * The Gemma project | ||
| * | ||
| * Copyright (c) 2012 University of British Columbia | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with | ||
| * the License. You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on | ||
| * an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the | ||
| * specific language governing permissions and limitations under the License. | ||
| */ | ||
| package ubic.gemma.core.analysis.expression.diff; | ||
|
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| import ubic.gemma.core.analysis.service.ExpressionDataMatrixService; | ||
| import ubic.gemma.core.datastructure.matrix.ExpressionDataDoubleMatrix; | ||
| import ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis; | ||
| import ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResult; | ||
| import ubic.gemma.model.analysis.expression.diff.HitListSize; | ||
| import ubic.gemma.model.common.quantitationtype.QuantitationType; | ||
| import ubic.gemma.model.expression.designElement.CompositeSequence; | ||
| import ubic.gemma.model.expression.experiment.ExperimentalFactor; | ||
| import ubic.gemma.model.expression.experiment.ExpressionExperiment; | ||
| import ubic.gemma.model.expression.experiment.ExpressionExperimentSubSet; | ||
| import ubic.gemma.model.genome.Gene; | ||
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| import java.util.Collection; | ||
| import java.util.Map; | ||
| import java.util.Set; | ||
|
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| /** | ||
| * @author paul | ||
| */ | ||
| @SuppressWarnings({ "unused", "WeakerAccess" }) // Possible external use | ||
| public interface DiffExAnalyzer { | ||
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| ExperimentalFactor determineInterceptFactor( Collection<ExperimentalFactor> factors, | ||
| QuantitationType quantitationType ); | ||
|
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| /** | ||
| * @param expressionExperiment the experiment | ||
| * @param config config | ||
| * @return analyses. There will be more than one if a subset factor is defined. | ||
| */ | ||
| Collection<DifferentialExpressionAnalysis> run( ExpressionExperiment expressionExperiment, | ||
| DifferentialExpressionAnalysisConfig config ); | ||
|
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| /*** | ||
| * Allows entry of modified data matrices into the workflow. | ||
| * @param config config | ||
| * @param expressionExperiment the experiment | ||
| * @param dmatrix D matrix | ||
| * @return analyses | ||
| */ | ||
| Collection<DifferentialExpressionAnalysis> run( ExpressionExperiment expressionExperiment, | ||
| ExpressionDataDoubleMatrix dmatrix, DifferentialExpressionAnalysisConfig config ); | ||
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| /** | ||
| * Generate HitListSize entities that will be stored to count the number of diff. ex probes at various preset | ||
| * thresholds, to avoid wasting time generating these counts on the fly later. This is done automatically during | ||
| * analysis, so is just here to allow 'backfilling'. | ||
| * | ||
| * @param probeToGeneMap map | ||
| * @param results results | ||
| * @return hit list sizes | ||
| */ | ||
| Set<HitListSize> computeHitListSizes( Collection<DifferentialExpressionAnalysisResult> results, | ||
| Map<CompositeSequence, Collection<Gene>> probeToGeneMap ); | ||
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| /** | ||
| * Utility method | ||
| * | ||
| * @param probeToGeneMap map | ||
| * @param resultList result list | ||
| * @return number of genes tested | ||
| */ | ||
| int getNumberOfGenesTested( Collection<DifferentialExpressionAnalysisResult> resultList, | ||
| Map<CompositeSequence, Collection<Gene>> probeToGeneMap ); | ||
|
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| /** | ||
| * this is needed so we can alter this in tests | ||
| * | ||
| * @param expressionDataMatrixService EE data matrix service | ||
| */ | ||
| void setExpressionDataMatrixService( ExpressionDataMatrixService expressionDataMatrixService ); | ||
|
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| /** | ||
| * Note that normally when we run a subset analysis, the subsetting is done internally, so we pass in the expression | ||
| * experiment, not the subset. This method is used for exceptions to that. | ||
| * | ||
| * @param subset subset | ||
| * @param config config | ||
| * @return analysis | ||
| */ | ||
| DifferentialExpressionAnalysis run( ExpressionExperimentSubSet subset, | ||
| DifferentialExpressionAnalysisConfig config ); | ||
|
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| } |
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