Package ubic.basecode.util.r

Class AbstractRClientTest

    • Field Detail

      • log

        protected static org.slf4j.Logger log

    • Constructor Detail

      • AbstractRClientTest

        public AbstractRClientTest()

    • Method Detail

      • 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()
        Like a two-sample t-test where the intercept is also of interest. @

      • 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. @

      • testLoadLibrary

        public void testLoadLibrary()

      • testStringListEval

        public void testStringListEval()

      • testStringListEvalB

        public void testStringListEvalB()

      • testTTest

        public void testTTest()

      • testTTestFail

        public void testTTestFail()