eqtlmappingpipeline.metaqtl4.MetaQTL4Settings Maven / Gradle / Ivy
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package eqtlmappingpipeline.metaqtl4;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import org.apache.commons.configuration.ConfigurationException;
import org.apache.commons.configuration.XMLConfiguration;
import umcg.genetica.io.Gpio;
import umcg.genetica.io.text.TextFile;
import umcg.genetica.io.trityper.util.ChrAnnotation;
/**
*
* @author harmjan
*/
public class MetaQTL4Settings {
// Output
private final boolean createSNPPValueSummaryStatisticsFile; // Output SNP P-Value summary statistics
private final boolean createSNPSummaryStatisticsFile; // Output SNP P-Value summary statistics
private final boolean createEQTLPValueTable; // Output an eQTL p-value table (only applies for a limited number (500) of SNP)
private final File outputReportsDir; // Output directory for reports
// SNP QC
// Analysis settings
private final boolean performParametricAnalysis; // Perform parametric analysis
private final boolean useAbsoluteZScorePValue; // Use absolute Z-score? (required for finding opposite allelic effects)
private final int ciseQTLAnalysMaxSNPProbeMidPointDistance; // Midpoint distance for declaring an eQTL effect CIS
private final int maxNrMostSignificantEQTLs; // Max number of results stored in memory
private final boolean performParametricAnalysisGetAccuratePValueEstimates; // Use an accurate estimation of the P-values
private final Integer nrThreads; // Use this number of threads
// Multiple testing correction
private final double fdrCutOff; // Cutoff for FDR procedure
private final int nrPermutationsFDR; // Number of permutations to determine FDR
// confinements
private final boolean performEQTLAnalysisOnSNPProbeCombinationSubset; // Confine to a certain set of probe/snp combinations?
private final Byte confineToSNPsThatMapToChromosome; // Confine SNP to be assessed to SNPs mapped on this chromosome
private final boolean expressionDataLoadOnlyProbesThatMapToChromosome; // Only load expression data for probes with a known chromosome mapping
// plots
private final double plotOutputPValueCutOff; // Use this p-value as a cutoff for drawing plots
private final String plotOutputDirectory; // Print the plots in this directory
private final boolean runOnlyPermutations;
private final Integer startWithPermutation;
private final Boolean confineSNPsToSNPsPresentInAllDatasets;
private final boolean confineProbesToProbesPresentInAllDatasets;
private final ArrayList datasetSettings;
private final String regressOutEQTLEffectFileName;
private final Double snpQCCallRateThreshold;
private final Double snpQCHWEThreshold;
private final Double snpQCMAFThreshold;
private final Byte confineToProbesThatMapToChromosome;
private final boolean createBinaryOutputFiles;
private final boolean createTEXTOutputFiles;
private File strConfineSNP;
private File strConfineProbe;
private File strSNPProbeConfine;
private final File probeAnnotationFile;
private final boolean provideFoldChangeData;
private final boolean provideBetasAndStandardErrors;
private final boolean equalRankForTies;
private final boolean createQQPlot;
private final boolean createDotPlot;
private final String settingsTextToReplace;
private final String settingsTextReplaceWith;
private final boolean cisAnalysis;
private final boolean transAnalysis;
public MetaQTL4Settings(String settings, String settingsTextToReplace, String settingsTextReplaceWith) throws IOException, Exception {
this.settingsTextToReplace = settingsTextToReplace;
this.settingsTextReplaceWith = settingsTextReplaceWith;
XMLConfiguration config = null;
try {
config = new XMLConfiguration(settings); // Use the apache XML configuration parser
} catch (ConfigurationException e) {
throw new Exception("Configuration not properly formatted: " + e.getMessage());
}
String analysisType = null;
String correlationType = null;
Boolean useAbsPVal = null;
Integer nrthread = null;
Integer cisDist = null;
Double MAF = null;
Double HWE = null;
Double callrate = null;
String correctiontype = null;
Double mtThreshold = null;
Integer numPermutations = null;
String outdir = null;
Double outputplotthreshold = null;
String outputplotdirectory = null;
// load the defaults:
performEQTLAnalysisOnSNPProbeCombinationSubset = false;
// QC defaults
try {
callrate = config.getDouble("defaults.qc.snpqccallratethreshold");
} catch (Exception e) {
}
if (callrate != null) {
snpQCCallRateThreshold = callrate;
} else {
snpQCCallRateThreshold = 0.95;
}
try {
HWE = config.getDouble("defaults.qc.snpqchwethreshold");
} catch (Exception e) {
}
if (HWE != null) {
snpQCHWEThreshold = HWE;
} else {
snpQCHWEThreshold = 0.0001;
}
String probeAnnot = null;
try {
probeAnnot = config.getString("defaults.analysis.probeAnnotationFile");
} catch (Exception e) {
}
probeAnnotationFile = new File(probeAnnot);
try {
MAF = config.getDouble("defaults.qc.snpqcmafthreshold");
} catch (Exception e) {
}
if (MAF != null) {
snpQCMAFThreshold = MAF;
} else {
snpQCMAFThreshold = 0.05;
}
// analysis settings
try {
analysisType = config.getString("defaults.analysis.analysistype");
} catch (Exception e) {
}
createQQPlot = config.getBoolean("defaults.analysis.createqqplot", false);
createDotPlot = config.getBoolean("defaults.analysis.createdotplot", false);
runOnlyPermutations = config.getBoolean("defaults.analysis.onlypermutations", false);
String strStartWithPermutation = null;
try {
strStartWithPermutation = config.getString("defaults.analysis.startwithpermutation", null);
if (settingsTextToReplace != null && strStartWithPermutation.contains(settingsTextToReplace)) {
strStartWithPermutation = strStartWithPermutation.replace(settingsTextToReplace, settingsTextReplaceWith);
}
} catch (Exception e) {
}
if (strStartWithPermutation != null) {
startWithPermutation = Integer.parseInt(strStartWithPermutation);
} else {
startWithPermutation = null;
}
if (analysisType != null) {
if (analysisType.toLowerCase().equals("cis")) {
cisAnalysis = true;
transAnalysis = false;
} else if (analysisType.toLowerCase().equals("trans")) {
cisAnalysis = false;
transAnalysis = true;
} else if (analysisType.toLowerCase().equals("cistrans")) {
cisAnalysis = true;
transAnalysis = true;
} else {
cisAnalysis = true;
transAnalysis = false;
}
} else {
cisAnalysis = true;
transAnalysis = false;
}
try {
cisDist = config.getInteger("defaults.analysis.cisanalysisprobedistance", null);
} catch (Exception e) {
}
if (cisDist != null) {
ciseQTLAnalysMaxSNPProbeMidPointDistance = cisDist;
} else {
ciseQTLAnalysMaxSNPProbeMidPointDistance = 250000;
}
try {
correlationType = config.getString("defaults.analysis.correlationtype");
} catch (Exception e) {
}
if (correlationType != null) {
if (correlationType.toLowerCase().equals("parametric")) {
performParametricAnalysis = true;
} else {
performParametricAnalysis = false;
}
} else {
performParametricAnalysis = false;
}
Boolean useIdenticalRanksForTies = null;
try {
useIdenticalRanksForTies = config.getBoolean("defaults.analysis.equalrankforties");
} catch (Exception e) {
}
if (useIdenticalRanksForTies != null) {
equalRankForTies = useIdenticalRanksForTies;
} else {
equalRankForTies = false;
}
try {
useAbsPVal = config.getBoolean("defaults.analysis.useabsolutepvalue");
} catch (Exception e) {
}
if (useAbsPVal == null) {
useAbsoluteZScorePValue = false;
} else {
useAbsoluteZScorePValue = useAbsPVal;
}
try {
nrthread = config.getInteger("defaults.analysis.threads", null);
} catch (Exception e) {
}
if (nrthread == null) {
nrThreads = (Runtime.getRuntime().availableProcessors() - 1);
} else {
int numProcs = Runtime.getRuntime().availableProcessors();
if (nrthread > numProcs || nrthread < 1) {
nrThreads = numProcs;
} else {
nrThreads = nrthread;
}
}
// multiple testing
try {
correctiontype = config.getString("defaults.multipletesting.type");
} catch (Exception e) {
}
if (correctiontype != null) {
} else {
}
try {
mtThreshold = config.getDouble("defaults.multipletesting.threshold", null);
} catch (Exception e) {
}
if (mtThreshold != null) {
fdrCutOff = mtThreshold;
} else {
fdrCutOff = 0.05;
}
try {
numPermutations = config.getInteger("defaults.multipletesting.permutations", null);
} catch (Exception e) {
}
if (numPermutations != null) {
nrPermutationsFDR = numPermutations;
} else {
nrPermutationsFDR = 0;
}
// output settings
try {
outdir = config.getString("defaults.output.outputdirectory");
if (settingsTextToReplace != null && outdir.contains(settingsTextToReplace)) {
outdir = outdir.replace(settingsTextToReplace, settingsTextReplaceWith);
}
} catch (Exception e) {
}
if (outdir != null) {
outputReportsDir = new File(outdir);
// check if dir exists. if it does not, create it:
if (!Gpio.exists(outdir)) {
Gpio.createOuputDir(outputReportsDir);
}
try {
config.save(new File(outputReportsDir, "metaqtlsettings.xml"));
} catch (ConfigurationException e) {
e.printStackTrace();
}
} else {
outputReportsDir = null;
System.out.println("Error: please supply an output directory.");
System.exit(-1);
}
// try {
// String probeConversionFileLoc = config.getString("defaults.analysis.probeconversion", null);
// if (probeConversionFileLoc != null && probeConversionFileLoc.length() > 0) {
// System.out.println(probeConversionFileLoc);
// }
//
// } catch (Exception e) {
// e.printStackTrace();
// System.exit(-1);
// }
try {
outputplotthreshold = config.getDouble("defaults.output.outputplotthreshold");
} catch (Exception e) {
}
createBinaryOutputFiles = config.getBoolean("defaults.output.binaryoutput", false);
createTEXTOutputFiles = config.getBoolean("defaults.output.textoutput", true);
if (outputplotthreshold != null) {
plotOutputPValueCutOff = outputplotthreshold;
} else {
plotOutputPValueCutOff = Double.MAX_VALUE;
}
try {
outputplotdirectory = config.getString("defaults.output.outputplotdirectory");
if (settingsTextToReplace != null && outputplotdirectory.contains(settingsTextToReplace)) {
outputplotdirectory = outputplotdirectory.replace(settingsTextToReplace, settingsTextReplaceWith);
}
} catch (Exception e) {
}
if (outputplotdirectory != null) {
plotOutputDirectory = Gpio.formatAsDirectory(outputplotdirectory);
} else {
plotOutputDirectory = outdir + "/plots/";
}
// check if dir exists. if it does not, create it if plots are requested
if (plotOutputPValueCutOff != Double.MAX_VALUE) {
if (!Gpio.exists(plotOutputDirectory)) {
Gpio.createDir(plotOutputDirectory);
}
}
createSNPPValueSummaryStatisticsFile = config.getBoolean("defaults.output.generatesnppvaluesummarystatistics", false);
provideFoldChangeData = config.getBoolean("defaults.output.generatefoldchangevalues", false);
provideBetasAndStandardErrors = config.getBoolean("defaults.output.generatebetaandfoldchanges", false);
createSNPSummaryStatisticsFile = config.getBoolean("defaults.output.generatesnpsummarystatistics", false);
createEQTLPValueTable = config.getBoolean("defaults.output.generateeqtlpvaluetable", false);
maxNrMostSignificantEQTLs = config.getInt("defaults.output.maxnreqtlresults", 150000);
expressionDataLoadOnlyProbesThatMapToChromosome = config.getBoolean("defaults.confine.confineProbesThatMapToKnownChromosome", true);
Boolean confineTpSNPsPresentInAllDs = config.getBoolean("defaults.confine.confineSNPsToSNPsPresentInAllDatasets", false);
confineSNPsToSNPsPresentInAllDatasets = confineTpSNPsPresentInAllDs;
confineToProbesThatMapToChromosome = null;
// confinements on snp, probe, or snp-probe
String confineSNP = null;
String confineProbe = null;
String snpProbeConfine = null;
// confine to this list of snp
try {
confineSNP = config.getString("defaults.confine.snp");
if (settingsTextToReplace != null && confineSNP.contains(settingsTextToReplace)) {
confineSNP = confineSNP.replace(settingsTextToReplace, settingsTextReplaceWith);
}
} catch (Exception e) {
}
// confine to this list of probes
try {
confineProbe = config.getString("defaults.confine.probe");
if (settingsTextToReplace != null && confineProbe.contains(settingsTextToReplace)) {
confineProbe = confineProbe.replace(settingsTextToReplace, settingsTextReplaceWith);
}
} catch (Exception e) {
}
// confine to this list of snp-probe combinations
try {
snpProbeConfine = config.getString("defaults.confine.snpProbe");
if (settingsTextToReplace != null && snpProbeConfine.contains(settingsTextToReplace)) {
snpProbeConfine = snpProbeConfine.replace(settingsTextToReplace, settingsTextReplaceWith);
}
} catch (Exception e) {
}
if (snpProbeConfine != null && snpProbeConfine.trim().length() > 0) {
strSNPProbeConfine = new File(snpProbeConfine);
}
if (confineSNP != null && confineSNP.trim().length() > 0) {
strConfineSNP = new File(confineSNP);
}
if (confineProbe != null && confineProbe.trim().length() > 0) {
strConfineProbe = new File(confineProbe);
}
// confine to snp present in all datasets
performParametricAnalysisGetAccuratePValueEstimates = false;
// confine to SNP that map to this chromosome
String confineStr = null;
try {
confineStr = config.getString("defaults.confine.confineToSNPsThatMapToChromosome", null);
} catch (Exception e) {
}
if (confineStr == null || confineStr.trim().length() == 0) {
confineToSNPsThatMapToChromosome = null;
} else {
byte chrConfine = ChrAnnotation.parseChr(confineStr);
if (chrConfine < 1) {
confineToSNPsThatMapToChromosome = null;
} else {
confineToSNPsThatMapToChromosome = chrConfine;
}
}
// confine to probes present in all datasets
confineProbesToProbesPresentInAllDatasets = config.getBoolean("defaults.confine.confineToProbesPresentInAllDatasets", false);
regressOutEQTLEffectFileName = config.getString("defaults.analysis.regressOutEQTLEffects");
// dataset parameters
int i = 0;
String dataset = config.getString("datasets.dataset(" + i + ").name"); // see if a dataset is defined
if (settingsTextToReplace != null && dataset.contains(settingsTextToReplace)) {
dataset = dataset.replace(settingsTextToReplace, settingsTextReplaceWith);
}
datasetSettings = new ArrayList();
while (dataset != null) {
String expressionData = null;
String genotypeLocation = null;
String genToExpCoupling = null;
String probeannotation = null;
String expressionplatform = null;
String gte = null;
// get the location of the expression data
try {
expressionData = config.getString("datasets.dataset(" + i + ").expressiondata");
if (settingsTextToReplace != null && expressionData.contains(settingsTextToReplace)) {
expressionData = expressionData.replace(settingsTextToReplace, settingsTextReplaceWith);
}
} catch (Exception e) {
}
if (expressionData != null) {
String expressionPlatform = null;
try {
expressionPlatform = config.getString("datasets.dataset(" + i + ").expressionplatform");
if (settingsTextToReplace != null && expressionData.contains(settingsTextToReplace)) {
expressionPlatform = expressionPlatform.replace(settingsTextToReplace, settingsTextReplaceWith);
}
} catch (Exception e) {
}
probeannotation = null;
try {
probeannotation = config.getString("datasets.dataset(" + i + ").probeannotation");
if (settingsTextToReplace != null && expressionData.contains(settingsTextToReplace)) {
probeannotation = probeannotation.replace(settingsTextToReplace, settingsTextReplaceWith);
}
if (probeannotation.length() == 0) {
probeannotation = null;
}
} catch (Exception e) {
}
expressionplatform = expressionPlatform;
}
// get the location of the dataset
try {
genotypeLocation = config.getString("datasets.dataset(" + i + ").location");
if (settingsTextToReplace != null && genotypeLocation.contains(settingsTextToReplace)) {
genotypeLocation = genotypeLocation.replace(settingsTextToReplace, settingsTextReplaceWith);
}
} catch (Exception e) {
System.out.println("Please provide a location on your disk where " + dataset + " is located");
System.exit(-1);
}
Gpio.formatAsDirectory(genotypeLocation);
// see if there is a genotype to expression couplings file
try {
genToExpCoupling = config.getString("datasets.dataset(" + i + ").genometoexpressioncoupling");
if (settingsTextToReplace != null && genToExpCoupling.contains(settingsTextToReplace)) {
genToExpCoupling = genToExpCoupling.replace(settingsTextToReplace, settingsTextReplaceWith);
}
} catch (Exception e) {
}
datasetSettings.add(new MetaQTL4DatasetSettings(dataset, genotypeLocation, expressionData, genToExpCoupling, expressionplatform));
dataset = null;
i++;
try {
dataset = config.getString("datasets.dataset(" + i + ").name");
if (settingsTextToReplace != null && dataset.contains(settingsTextToReplace)) {
dataset = dataset.replace(settingsTextToReplace, settingsTextReplaceWith);
}
} catch (Exception e) {
}
}
}
public String summarize() {
String summary = "Following settings will be applied:\n"
+ "Settings\n----\n"
+ "settingsTextToReplace\t" + settingsTextToReplace + "\n"
+ "settingsTextReplaceWith\t" + settingsTextReplaceWith + "\n"
+ "\nOutput\n----\n"
+ "createSNPPValueSummaryStatisticsFile\t" + createSNPPValueSummaryStatisticsFile + "\n"
+ "createEQTLPValueTable\t" + createEQTLPValueTable + "\n"
+ "outputReportsDir\t" + outputReportsDir + "\n"
+ "\nAnalysis\n----\n"
+ "performCiseQTLAnalysis\t" + cisAnalysis + "\n"
+ "performTranseQTLAnalysis\t" + transAnalysis + "\n"
+ "performParametricAnalysis\t" + performParametricAnalysis + "\n"
+ "useAbsoluteZScorePValue\t" + useAbsoluteZScorePValue + "\n"
+ "ciseQTLAnalysMaxSNPProbeMidPointDistance\t" + ciseQTLAnalysMaxSNPProbeMidPointDistance + "\n"
+ "maxNrMostSignificantEQTLs\t" + maxNrMostSignificantEQTLs + "\n"
+ "performParametricAnalysisGetAccuratePValueEstimates\t" + performParametricAnalysisGetAccuratePValueEstimates + "\n"
+ "nrThreads\t" + nrThreads + "\n"
+ "fdrCutOff\t" + fdrCutOff + "\n"
+ "nrPermutationsFDR\t" + nrPermutationsFDR + "\n"
+ "regressOutEQTLEffectFileName\t" + regressOutEQTLEffectFileName + "\n"
+ "snpQCCallRateThreshold\t" + snpQCCallRateThreshold + "\n"
+ "snpQCHWEThreshold\t" + snpQCHWEThreshold + "\n"
+ "snpQCMAFThreshold\t" + snpQCMAFThreshold + "\n"
+ "\nConfinements\n----\n"
+ "performEQTLAnalysisOnSNPProbeCombinationSubset\t" + performEQTLAnalysisOnSNPProbeCombinationSubset + "\n"
+ "confineToSNPsThatMapToChromosome\t" + confineToSNPsThatMapToChromosome + "\n"
+ "expressionDataLoadOnlyProbesThatMapToChromosome\t" + expressionDataLoadOnlyProbesThatMapToChromosome + "\n"
// + "tsSNPsConfine\t" +tsSNPsConfine+ "\n"
// + "tsProbesConfine\t" +tsProbesConfine+ "\n"
// + "tsSNPProbeCombinationsConfine\t" +tsSNPProbeCombinationsConfine+ "\n"
+ "confineSNPsToSNPsPresentInAllDatasets\t" + confineSNPsToSNPsPresentInAllDatasets + "\n"
+ "confineProbesToProbesPresentInAllDatasets\t" + confineProbesToProbesPresentInAllDatasets + "\n"
+ "confineToProbesThatMapToChromosome\t" + confineToProbesThatMapToChromosome + "\n"
+ "expressionDataLoadOnlyProbesThatMapToChromosome\t" + expressionDataLoadOnlyProbesThatMapToChromosome + "\n"
+ "\n";
summary += "\nDatasets\n----\n";
for (MetaQTL4DatasetSettings settings : this.datasetSettings) {
summary += "DatasetName\t" + settings.getName() + "\n";
summary += "ExpressionData\t" + settings.getTraitDataLocation() + "\n";
summary += "ExpressionPlatform\t" + settings.getAnnotationFile() + "\n";
summary += "GenotypeData\t" + settings.getGenotypeLocation() + "\n";
summary += "GTE\t" + settings.getGenotypeToTraitCoupling() + "\n";
}
return summary;
}
public void writeSettingsToDisk() throws Exception {
TextFile tf = new TextFile(this.outputReportsDir + "/UsedSettings.txt", TextFile.W);
tf.write(summarize());
tf.close();
}
public String getSettingsTextToReplace() {
return settingsTextToReplace;
}
public String getSettingsTextReplaceWith() {
return settingsTextReplaceWith;
}
public boolean isCreateSNPPValueSummaryStatisticsFile() {
return createSNPPValueSummaryStatisticsFile;
}
public boolean isCreateSNPSummaryStatisticsFile() {
return createSNPSummaryStatisticsFile;
}
public boolean isCreateEQTLPValueTable() {
return createEQTLPValueTable;
}
public File getOutputReportsDir() {
return outputReportsDir;
}
public boolean isPerformParametricAnalysis() {
return performParametricAnalysis;
}
public boolean isUseAbsoluteZScorePValue() {
return useAbsoluteZScorePValue;
}
public int getCiseQTLAnalysMaxSNPProbeMidPointDistance() {
return ciseQTLAnalysMaxSNPProbeMidPointDistance;
}
public int getMaxNrMostSignificantEQTLs() {
return maxNrMostSignificantEQTLs;
}
public boolean isPerformParametricAnalysisGetAccuratePValueEstimates() {
return performParametricAnalysisGetAccuratePValueEstimates;
}
public Integer getNrThreads() {
return nrThreads;
}
public double getFdrCutOff() {
return fdrCutOff;
}
public int getNrPermutationsFDR() {
return nrPermutationsFDR;
}
public boolean isPerformEQTLAnalysisOnSNPProbeCombinationSubset() {
return performEQTLAnalysisOnSNPProbeCombinationSubset;
}
public Byte getConfineToSNPsThatMapToChromosome() {
return confineToSNPsThatMapToChromosome;
}
public boolean isExpressionDataLoadOnlyProbesThatMapToChromosome() {
return expressionDataLoadOnlyProbesThatMapToChromosome;
}
public double getPlotOutputPValueCutOff() {
return plotOutputPValueCutOff;
}
public String getPlotOutputDirectory() {
return plotOutputDirectory;
}
public boolean isRunOnlyPermutations() {
return runOnlyPermutations;
}
public Integer getStartWithPermutation() {
return startWithPermutation;
}
public Boolean getConfineSNPsToSNPsPresentInAllDatasets() {
return confineSNPsToSNPsPresentInAllDatasets;
}
public boolean isConfineProbesToProbesPresentInAllDatasets() {
return confineProbesToProbesPresentInAllDatasets;
}
public ArrayList getDatasetSettings() {
return datasetSettings;
}
public String getRegressOutEQTLEffectFileName() {
return regressOutEQTLEffectFileName;
}
public Double getSnpQCCallRateThreshold() {
return snpQCCallRateThreshold;
}
public Double getSnpQCHWEThreshold() {
return snpQCHWEThreshold;
}
public Double getSnpQCMAFThreshold() {
return snpQCMAFThreshold;
}
public Byte getConfineToProbesThatMapToChromosome() {
return confineToProbesThatMapToChromosome;
}
public boolean isCreateBinaryOutputFiles() {
return createBinaryOutputFiles;
}
public boolean isCreateTEXTOutputFiles() {
return createTEXTOutputFiles;
}
public File getConfineSNPFile() {
return strConfineSNP;
}
public File getConfineProbeFile() {
return strConfineProbe;
}
public boolean isProvideFoldChangeData() {
return provideFoldChangeData;
}
public boolean isProvideBetasAndStandardErrors() {
return provideBetasAndStandardErrors;
}
public boolean isEqualRankForTies() {
return equalRankForTies;
}
public boolean isCreateQQPlot() {
return createQQPlot;
}
public boolean isCreateDotPlot() {
return createDotPlot;
}
public File getSNPProbeConfineFile() {
return strSNPProbeConfine;
}
public boolean isCisAnalysis() {
return cisAnalysis;
}
public boolean isTransAnalysis() {
return transAnalysis;
}
public int getNrDatasets() {
return datasetSettings.size();
}
public File getProbeAnnotationFile() {
return probeAnnotationFile;
}
}
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