Package ubic.basecode.math.linearmodels

Class MeanVarianceEstimatorTest

java.lang.Object

ubic.basecode.math.linearmodels.MeanVarianceEstimatorTest

public class MeanVarianceEstimatorTest
extends Object

Author:

ptan

Constructor Summary

Constructors

Constructor	Description
MeanVarianceEstimatorTest()

Method Summary

Modifier and Type	Method	Description
void	testDuplicateRows()	Duplicate row
void	testInterpolate()	Tests two things: 1.
void	testMeanVarianceNoDesignWithColsRowAllMissing()	Data has missing values, no Design matrix provided so plot a generic mean-variance plot
void	testMeanVarianceNoDesignWithMissing()	Data has missing values, no Design matrix provided so plot a generic mean-variance plot (no voom)
void	testVoom()	Test calculation of weights for LeastSquaresFitting.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MeanVarianceEstimatorTest

public MeanVarianceEstimatorTest()

Method Detail

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) f<-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