Package ubic.basecode.math.linearmodels

Class MeanVarianceEstimatorTest

java.lang.Object
ubic.basecode.math.linearmodels.MeanVarianceEstimatorTest
public class MeanVarianceEstimatorTest extends Object
Author:
ptan

  • Constructor Details

    • MeanVarianceEstimatorTest

      public MeanVarianceEstimatorTest()

  • Method Details

    • testInterpolate

      public void testInterpolate() throws Exception
      Tests two things: 1. Input data's X values are not sorted 2. Interpolated X values are outside the domain.
      Throws:
      Exception - R code: x = c(9.0, 8.0, 7.0, 6.0, 5.0, 4.0, 3.0, 2.0, 1.0, 0.0) y = c(1.0, 0.25, 0.1111111111111111, 0.0625, 0.04, 0.027777777777777776, 0.02040816326530612, 0.015625, 0.012345679012345678, 0.01) interpolate = c(9.5, 8.5, 7.5, 6.5, 5.5, 4.5, 3.5, 2.5, 1.5, 0.5) finvalid input: '<'-approxfun(x,y,rule=2) f(c(interpolate))

    • testDuplicateRows

      public void testDuplicateRows() throws Exception
      Duplicate row
      Throws:
      Exception

    • testVoom

      public void testVoom() throws Exception
      Test calculation of weights for LeastSquaresFitting. See test-squeezevar.R
      Throws:
      Exception

    • testMeanVarianceNoDesignWithColsRowAllMissing

      public void testMeanVarianceNoDesignWithColsRowAllMissing() throws Exception
      Data has missing values, no Design matrix provided so plot a generic mean-variance plot
      Throws:
      Exception

    • testMeanVarianceNoDesignWithMissing

      public void testMeanVarianceNoDesignWithMissing() throws Exception
      Data has missing values, no Design matrix provided so plot a generic mean-variance plot (no voom)
      Throws:
      Exception