Examples with FactorValue ubic.gemma.model.expression.experiment.FactorValue used on opensource projects

Example 6 with FactorValue

use of ubic.gemma.model.expression.experiment.FactorValue in project Gemma by PavlidisLab.

the class OneWayAnovaAnalyzerTest method testOnewayAnovaB.

@Test
public void testOnewayAnovaB() throws Exception {
    if (!connected) {
        log.warn("Could not establish R connection.  Skipping test ...");
        return;
    }
    super.configureTestDataForOneWayAnova();
    this.configureMocks();
    /*
         * Add a factor with three levels
         */
    ExperimentalFactor experimentalFactorC = ExperimentalFactor.Factory.newInstance();
    experimentalFactorC.setName("groupash");
    experimentalFactorC.setId(5399424551L);
    experimentalFactorC.setType(FactorType.CATEGORICAL);
    expressionExperiment.getExperimentalDesign().getExperimentalFactors().add(experimentalFactorC);
    FactorValue controlGroup = null;
    for (int i = 1; i <= 3; i++) {
        FactorValue f = FactorValue.Factory.newInstance();
        f.setId(2000L + i);
        if (i != 2) {
            f.setValue(i + "_group");
        } else {
            f.setValue("control_group");
            controlGroup = f;
        }
        f.setExperimentalFactor(experimentalFactorC);
        experimentalFactorC.getFactorValues().add(f);
    }
    List<FactorValue> facV = new ArrayList<>(experimentalFactorC.getFactorValues());
    for (int i = 0; i < 8; i++) {
        super.biomaterials.get(i).getFactorValues().add(facV.get(i % 3));
    }
    Collection<ExperimentalFactor> factors = new HashSet<>();
    factors.add(experimentalFactorC);
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.setFactorsToInclude(factors);
    Collection<DifferentialExpressionAnalysis> expressionAnalyses = analyzer.run(expressionExperiment, config);
    DifferentialExpressionAnalysis expressionAnalysis = expressionAnalyses.iterator().next();
    Collection<ExpressionAnalysisResultSet> resultSets = expressionAnalysis.getResultSets();
    ExpressionAnalysisResultSet resultSet = resultSets.iterator().next();
    int numResults = resultSet.getResults().size();
    assertEquals(100, numResults);
    assertEquals(controlGroup, resultSet.getBaselineGroup());
    factors = resultSet.getExperimentalFactors();
    assertEquals(1, factors.size());
    for (DifferentialExpressionAnalysisResult r : resultSet.getResults()) {
        CompositeSequence probe = r.getProbe();
        Double pvalue = r.getPvalue();
        // if ( pvalue != null ) assertNotNull( stat );
        assertNotNull(probe);
        switch(probe.getName()) {
            case "probe_98":
                assertEquals(0.1604, pvalue, 0.001);
                break;
            case "probe_10":
                assertEquals(0.8014, pvalue, 0.0001);
                break;
            case "probe_4":
                assertEquals(0.6531, pvalue, 0.0001);
                break;
        }
    }
}

Example 7 with FactorValue

use of ubic.gemma.model.expression.experiment.FactorValue in project Gemma by PavlidisLab.

the class AuditAdviceTest method checkEEAuditTrails.

private void checkEEAuditTrails(ExpressionExperiment ee, Collection<Long> trailIds, Collection<Long> eventIds) {
    this.checkAuditTrail(ee, trailIds, eventIds);
    for (BioAssay ba : ee.getBioAssays()) {
        this.checkAuditTrail(ba, trailIds, eventIds);
        BioMaterial bm = ba.getSampleUsed();
        this.checkAuditTrail(bm, trailIds, eventIds);
        for (Characteristic c : bm.getCharacteristics()) {
            this.checkAuditTrail(c, trailIds, eventIds);
        }
        for (Treatment t : bm.getTreatments()) {
            this.checkAuditTrail(t, trailIds, eventIds);
            this.checkAuditTrail(t.getAction(), trailIds, eventIds);
        // for ( CompoundMeasurement cm : t.getCompoundMeasurements() ) {
        // checkAuditTrail( cm.getCompound().getCompoundIndices(), trailIds, eventIds );
        // }
        }
    }
    Collection<ExperimentalFactor> experimentalFactors = ee.getExperimentalDesign().getExperimentalFactors();
    assertTrue(experimentalFactors.size() > 0);
    for (ExperimentalFactor ef : experimentalFactors) {
        this.checkAuditTrail(ef, trailIds, eventIds);
        for (FactorValue fv : ef.getFactorValues()) {
            for (Characteristic c : fv.getCharacteristics()) {
                this.checkAuditTrail(c, trailIds, eventIds);
            }
        }
    }
}

Example 8 with FactorValue

use of ubic.gemma.model.expression.experiment.FactorValue in project Gemma by PavlidisLab.

the class DatabaseViewGeneratorImpl method generateDifferentialExpressionView.

private void generateDifferentialExpressionView(Integer limit, Collection<ExpressionExperiment> experiments) throws IOException {
    DatabaseViewGeneratorImpl.log.info("Generating dataset diffex view");
    /*
         * Get handle to output file
         */
    File file = this.getViewFile(DatabaseViewGeneratorImpl.DATASET_DIFFEX_VIEW_BASENAME);
    DatabaseViewGeneratorImpl.log.info("Writing to " + file);
    try (Writer writer = new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(file)))) {
        /*
             * For each gene that is differentially expressed, print out a line per contrast
             */
        writer.write("GemmaDsId\tEEShortName\tGeneNCBIId\tGemmaGeneId\tFactor\tFactorURI\tBaseline\tContrasting\tDirection\n");
        int i = 0;
        for (ExpressionExperiment ee : experiments) {
            ee = expressionExperimentService.thawLite(ee);
            Collection<DifferentialExpressionAnalysis> results = differentialExpressionAnalysisService.getAnalyses(ee);
            if (results == null || results.isEmpty()) {
                DatabaseViewGeneratorImpl.log.warn("No differential expression results found for " + ee);
                continue;
            }
            // noinspection StatementWithEmptyBody // FIXME. Should probably skip for this purpose.
            if (results.size() > 1) {
            }
            DatabaseViewGeneratorImpl.log.info("Processing: " + ee.getShortName());
            for (DifferentialExpressionAnalysis analysis : results) {
                analysis = this.differentialExpressionAnalysisService.thawFully(analysis);
                for (ExpressionAnalysisResultSet ears : analysis.getResultSets()) {
                    // ears = differentialExpressionResultService.thawRawAndProcessed( ears );
                    FactorValue baselineGroup = ears.getBaselineGroup();
                    if (baselineGroup == null) {
                        // log.warn( "No baseline defined for " + ee ); // interaction
                        continue;
                    }
                    if (ExperimentalDesignUtils.isBatch(baselineGroup.getExperimentalFactor())) {
                        continue;
                    }
                    String baselineDescription = ExperimentalDesignUtils.prettyString(baselineGroup);
                    // Get the factor category name
                    StringBuilder factorName = new StringBuilder();
                    StringBuilder factorURI = new StringBuilder();
                    for (ExperimentalFactor ef : ears.getExperimentalFactors()) {
                        factorName.append(ef.getName()).append(",");
                        if (ef.getCategory() instanceof VocabCharacteristic) {
                            factorURI.append(ef.getCategory().getCategoryUri()).append(",");
                        }
                    }
                    factorName = new StringBuilder(StringUtils.removeEnd(factorName.toString(), ","));
                    factorURI = new StringBuilder(StringUtils.removeEnd(factorURI.toString(), ","));
                    if (ears.getResults() == null || ears.getResults().isEmpty()) {
                        DatabaseViewGeneratorImpl.log.warn("No  differential expression analysis results found for " + ee);
                        continue;
                    }
                    // Generate probe details
                    for (DifferentialExpressionAnalysisResult dear : ears.getResults()) {
                        if (dear == null) {
                            DatabaseViewGeneratorImpl.log.warn("Missing results for " + ee + " skipping to next. ");
                            continue;
                        }
                        if (dear.getCorrectedPvalue() == null || dear.getCorrectedPvalue() > DatabaseViewGeneratorImpl.THRESH_HOLD)
                            continue;
                        String formatted = this.formatDiffExResult(ee, dear, factorName.toString(), factorURI.toString(), baselineDescription);
                        if (StringUtils.isNotBlank(formatted))
                            writer.write(formatted);
                    }
                // dear loop
                }
            // ears loop
            }
            if (limit != null && (limit > 0 && ++i > limit))
                break;
        }
    // EE loop
    }
}

Example 9 with FactorValue

use of ubic.gemma.model.expression.experiment.FactorValue in project Gemma by PavlidisLab.

the class DatabaseViewGeneratorImpl method formatDiffExResult.

private String formatDiffExResult(ExpressionExperiment ee, DifferentialExpressionAnalysisResult probeAnalysisResult, String factorName, String factorURI, String baselineDescription) {
    CompositeSequence cs = probeAnalysisResult.getProbe();
    Collection<Gene> genes = compositeSequenceService.getGenes(cs);
    if (genes.isEmpty() || genes.size() > 1) {
        return null;
    }
    Gene g = genes.iterator().next();
    if (g.getNcbiGeneId() == null)
        return null;
    Collection<ContrastResult> contrasts = probeAnalysisResult.getContrasts();
    StringBuilder buf = new StringBuilder();
    for (ContrastResult cr : contrasts) {
        FactorValue factorValue = cr.getFactorValue();
        String direction = cr.getLogFoldChange() < 0 ? "-" : "+";
        String factorValueDescription = ExperimentalDesignUtils.prettyString(factorValue);
        buf.append(String.format("%d\t%s\t%s\t%d\t%s\t%s\t%s\t%s\t%s\n", ee.getId(), ee.getShortName(), g.getNcbiGeneId().toString(), g.getId(), factorName, factorURI, baselineDescription, factorValueDescription, direction));
    }
    return buf.toString();
}

Example 10 with FactorValue

use of ubic.gemma.model.expression.experiment.FactorValue in project Gemma by PavlidisLab.

the class FactorValueVector method buildKey.

private String buildKey() {
    StringBuilder buf = new StringBuilder();
    buf.append("[");
    for (Iterator<ExperimentalFactor> i = factors.iterator(); i.hasNext(); ) {
        ExperimentalFactor factor = i.next();
        buf.append(factor.getCategory());
        buf.append(factor.getName()).append(" (").append(factor.getDescription()).append(")");
        buf.append(" => [ ");
        for (Iterator<FactorValue> it = this.getValuesForFactor(factor).iterator(); it.hasNext(); ) {
            buf.append(it.next());
            if (it.hasNext())
                buf.append(", ");
        }
        buf.append(" ] ");
        if (i.hasNext())
            buf.append("; ");
    }
    buf.append("]");
    return buf.toString();
}