Examples of org.broad.igv.data.Dataset

org.broad.igv.data.Dataset
A dataset is an in-memory representation of a numerical dataset. It is used for non-indexed data formats that are read into memory as opposed to read off disk as needed. The use of objects is eschewed in favor of simple arrays to minimize memory. @author jrobinso

        String input = "formatexp " + inputFile + " " + outputFile;
        igvTools.run(input.split("\\s+"));
        Genome genome = TestUtils.loadGenome();


        ExpressionFileParser parser = new ExpressionFileParser(new ResourceLocator(outputFile), null, genome);
        Dataset ds = parser.createDataset();
        assertEquals(10, ds.getChromosomes().length);
    }

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        ExpressionFormatter formatter = new ExpressionFormatter();
        formatter.convert(inputFile, outputFile, ExpressionFormatter.FileType.GCT);


        ExpressionFileParser parser = new ExpressionFileParser(new ResourceLocator(outputPath), null, genome);
        Dataset ds = parser.createDataset();
        assertTrue(ds.getDataMax() > 0);
        assertTrue(ds.getDataMin() < 0);
        //Should this be true?
        //assertTrue(ds.isLogNormalized());
    }

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Related Classes of org.broad.igv.data.Dataset

org.broad.igv.tools.converters.ExpressionFormatterTest

org.broad.igv.tools.IGVToolsTest

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