Package ubic.basecode.util.r

Class AbstractRClientTest

java.lang.Object
ubic.basecode.util.r.AbstractRClientTest
Direct Known Subclasses:
JRIClientTest, RServeClientTest
public abstract class AbstractRClientTest extends Object
Author:
Paul

  • Field Details

    • log

      protected static org.slf4j.Logger log

  • Constructor Details

    • AbstractRClientTest

      public AbstractRClientTest()

  • Method Details

    • setUp

      public void setUp() throws IOException
      Throws:
      IOException

    • tearDown

      public void tearDown()

    • createRClient

      protected abstract AbstractRClient createRClient()

    • testAnovaA

      public void testAnovaA()

    • testAnovaB

      public void testAnovaB()

    • testAnovaC

      public void testAnovaC()

    • testAnovaD

      public void testAnovaD()

    • testAnovaE

      public void testAnovaE()

    • testAnovaF

      public void testAnovaF()
      One way @

    • testAssignAndRetrieveMatrix

      public void testAssignAndRetrieveMatrix()

    • testAssignAndRetrieveMatrixB

      public void testAssignAndRetrieveMatrixB()

    • testAssignAndRetrieveMatrixC

      public void testAssignAndRetrieveMatrixC()

    • testAssignAndRetrieveMatrixD

      public void testAssignAndRetrieveMatrixD()

    • testAssignStringList

      public void testAssignStringList()

    • testDataFrameA

      public void testDataFrameA()

    • testDoubleArrayTwoDoubleArrayEval

      public void testDoubleArrayTwoDoubleArrayEval()

    • testDoubleTwoDoubleArrayEval

      public void testDoubleTwoDoubleArrayEval()

    • testExec

      public void testExec()

    • testExecDoubleArray

      public void testExecDoubleArray()

    • testExecError

      public void testExecError()

    • testFactorAssign

      public void testFactorAssign()

    • testFindExecutable

      public void testFindExecutable() throws Exception
      Throws:
      Exception

    • testLimmaA

      public void testLimmaA() throws Exception
      Also exercises dataFrameEval 
       library(limma)

 dat<-read.table("data/testdata.txt", header=T, row.names=1)

 f1<-factor(c("A", "A", "A", "A", "A", "A", "B", "B", "B", "B", "B", "B"));

 f2<-factor(c("X", "X", "Y", "Y", "Z", "Z", "X", "X", "Y", "Y", "Z", "Z"));

 cov1<-c( -0.230 , 1.400, -0.210, 0.570, -0.064, 0.980 ,-0.082, -0.094, 0.630, -2.000, 0.640, -0.870);

 mo<-model.matrix(˜ f1 + f2 + cov1 - 1);

 contr<-makeContrasts(A-B, levels=mo);

 fit<-lmFit(dat, mo);

 fit<-contrasts.fit(fit, contr);

 fit<-eBayes(fit)

 res<-topTable(fit)
      Throws:
      Exception

    • testLinearModelA

      public void testLinearModelA() throws org.rosuda.REngine.REXPMismatchException
      Like a two-sample t-test where the intercept is also of interest. @
      Throws:
      org.rosuda.REngine.REXPMismatchException

    • testLinearModelB

      public void testLinearModelB()
      With a continuous covariate as well a categorical one. @

    • testLinearModelC

      public void testLinearModelC()

    • testLinearModelD

      public void testLinearModelD()
      Basically a one-way anova with 4 levels in the factor. @

    • testListEvalA

      public void testListEvalA() throws Exception
      Throws:
      Exception

    • testListEvalB

      public void testListEvalB() throws Exception
      Throws:
      Exception

    • testLoadLibrary

      public void testLoadLibrary()

    • testLoadScript

      public void testLoadScript() throws Exception
      Throws:
      Exception

    • testStringListEval

      public void testStringListEval()

    • testStringListEvalB

      public void testStringListEvalB()

    • testTTest

      public void testTTest()

    • testTTestFail

      public void testTTestFail()