Examples with FilterConfig ubic.gemma.core.analysis.preprocess.filter.FilterConfig used on opensource projects

Example 1 with FilterConfig

use of ubic.gemma.core.analysis.preprocess.filter.FilterConfig in project Gemma by PavlidisLab.

the class ExpressionDataFileServiceImpl method getDataMatrix.

private ExpressionDataDoubleMatrix getDataMatrix(ExpressionExperiment ee, boolean filtered) {
    ee = expressionExperimentService.thawLite(ee);
    ExpressionDataDoubleMatrix matrix;
    if (filtered) {
        FilterConfig filterConfig = new FilterConfig();
        filterConfig.setIgnoreMinimumSampleThreshold(true);
        filterConfig.setIgnoreMinimumRowsThreshold(true);
        matrix = expressionDataMatrixService.getFilteredMatrix(ee, filterConfig);
    } else {
        matrix = expressionDataMatrixService.getProcessedExpressionDataMatrix(ee);
    }
    return matrix;
}

Example 2 with FilterConfig

use of ubic.gemma.core.analysis.preprocess.filter.FilterConfig in project Gemma by PavlidisLab.

the class SampleCoexpressionMatrixServiceImpl method loadFilteredMatrix.

private ExpressionDataDoubleMatrix loadFilteredMatrix(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors, boolean requireSequences) {
    FilterConfig fConfig = new FilterConfig();
    fConfig.setIgnoreMinimumRowsThreshold(true);
    fConfig.setIgnoreMinimumSampleThreshold(true);
    fConfig.setRequireSequences(// not sure if this is the best thing to do. Some tests will fail.
    requireSequences);
    // Loads using new array designs will fail. So we allow special case where there are no sequences.
    return expressionDataMatrixService.getFilteredMatrix(ee, fConfig, vectors);
}

Example 3 with FilterConfig

use of ubic.gemma.core.analysis.preprocess.filter.FilterConfig in project Gemma by PavlidisLab.

the class LinkAnalysisController method run.

public String run(Long id) {
    /* this 'run' method is exported in the spring-beans.xml */
    ExpressionExperiment ee = expressionExperimentService.load(id);
    if (ee == null) {
        throw new IllegalArgumentException("Cannot access experiment with id=" + id);
    }
    experimentReportService.evictFromCache(id);
    LinkAnalysisConfig lac = new LinkAnalysisConfig();
    FilterConfig fc = new FilterConfig();
    LinkAnalysisTaskCommand cmd = new LinkAnalysisTaskCommand(ee, lac, fc);
    return taskRunningService.submitRemoteTask(cmd);
}