CalculationThread(
int i,
LinkedBlockingQueue<WorkPackage> packageQueue,
LinkedBlockingQueue<WorkPackage> resultQueue,
TriTyperExpressionData[] expressiondata,
DoubleMatrixDataset<String, String>[] covariates,
IntMatrix2D probeTranslationTable,
int[][] expressionToGenotypeIds,
Settings settings,
EQTLPlotter plotter,
boolean binaryoutput,
boolean useAbsoluteZScores,
boolean testSNPsPresentInBothDatasets) {
// m_binaryoutput = binaryoutput;
m_name = i;
m_workpackage_queue = packageQueue;
m_result_queue = resultQueue;
m_probeTranslation = probeTranslationTable;
m_expressiondata = expressiondata;
boolean m_cis = settings.cisAnalysis;
boolean m_trans = settings.transAnalysis;
metaAnalyseInteractionTerms = settings.metaAnalyseInteractionTerms;
metaAnalyseModelCorrelationYHat = settings.metaAnalyseModelCorrelationYHat;
m_useAbsoluteZScores = useAbsoluteZScores;
m_name = i;
m_numProbes = m_probeTranslation.columns();
m_numDatasets = m_probeTranslation.rows();
m_expressionToGenotypeIds = expressionToGenotypeIds;
// probeVariance = new double[m_numDatasets][0];
// probeMean = new double[m_numDatasets][0];
// probeName = new String[m_numDatasets][0];
// for (int d = 0; d < m_numDatasets; d++) {
// probeVariance[d] = expressiondata[d].getProbeVariance();
// probeMean[d] = expressiondata[d].getProbeMean();
// probeName[d] = expressiondata[d].getProbes();
// }
m_covariates = covariates;
this.testSNPsPresentInBothDatasets = testSNPsPresentInBothDatasets;
cisOnly = false;
// cisTrans = false;
transOnly = false;
determinebeta = settings.provideBetasAndStandardErrors;
determinefoldchange = settings.provideFoldChangeData;
if (m_cis && !m_trans) {
cisOnly = true;
} else if (!m_cis && m_trans) {
transOnly = true;
}
// else if (m_cis && m_trans) {
// cisTrans = true;
// }
m_eQTLPlotter = plotter;
m_pvaluePlotThreshold = settings.plotOutputPValueCutOff;
// if (covariates != null) {
// try {
// rConnection = new RConnection();
// REXP x = rConnection.eval("R.version.string");
// System.out.println("Thread made R Connection: " + x.asString());
//// rConnection.voidEval("install.packages('sandwich')");
// rConnection.voidEval("library(sandwich)");
// } catch (RserveException ex) {
// Logger.getLogger(CalculationThread.class.getName()).log(Level.SEVERE, null,
// ex);
// rConnection = null;
// } catch (REXPMismatchException ex) {
// Logger.getLogger(CalculationThread.class.getName()).log(Level.SEVERE, null,
// ex);
// rConnection = null;
// }
// }
}
