.RCMloss-method         Internal function
CNGEheatmaps            Parellel CN and GE heatmap plotting
ExpressionSet2order     Genomic ordering of ExpressionSet-objects.
ExpressionSet2subset    Subsetting ExpressionSet-objects.
ExpressionSet2weightedSubset
                        Weighted subsetting ExpressionSet-objects.
RCMestimation           Fitting of the random coefficients model.
RCMrandom               Random data from the random coefficients model.
RCMrandom-method        Methods for Function RCMrandom
RCMtest                 Hypothesis testing within the random
                        coefficient model.
cghCall2cghSeg          Genomic ordering of cghSeg-objects.
cghCall2maximumSubset   Maximum subsetting cghCall-objects.
cghCall2order           Genomic ordering of cghCall-objects.
cghCall2subset          Subsetting cghCall-objects.
cghCall2weightedSubset
                        Weighted subsetting cghCall-objects.
cghSeg2order            Genomic ordering of cghSeg-objects.
cghSeg2subset           Subsetting cghSeg-objects.
cghSeg2weightedSubset   Weighted subsetting cghSeg-objects.
cisEffectPlot           DNA-mRNA plot
cisEffectTable          Table of cis-effect test results
cisEffectTest           Nonparametric testing for copy number induced
                        differential gene expression.
cisEffectTune           Pre-test and tuning.
cisTest-class           Class "cisTest" for storing the results of the
                        function cisEffectTest.
entTest-class           Class "entTest" for storing the results of the
                        function entropyTest.
entropyTest             One-sided two-sample test for entropy
                        comparison
expandMatching2singleIDs
                        Expand matching to single entries
getSegFeatures          Identical signature features selection from
                        cghCall-object.
hdEntropy               Entropy estimation.
hdMI                    Mutual information estimation.
matchAnn2Ann            Genomic location matching of two sets of
                        features
matchCGHcall2ExpressionSet
                        Genomic location matching of CN and GE data
merge2ExpressionSets    Merge two ExpressionSet-objects into one
                        ExpressionSet-object
merge2cghCalls          Merge two cghCall-objects into one
                        cghCall-object
miTest-class            Class "miTest" for storing the results of the
                        function mutInfTest.
mutInfTest              Test for mutual information
nBreakpoints            Number of breakpoints
pathway1sample          Penalized estimation of a pathyway's regulatory
                        network from DNA copy number and gene
                        expression data (one-sample).
pathway2sample          Penalized estimation of a pathyway's regulatory
                        network from DNA copy number and gene
                        expression data (two-sample).
pathwayFit-class        Class "pathwayFit" for storing the results of
                        the function pathway1sample or pathway2sample.
pathwayPlot             Plot of the pathyway topology as reconstructed
                        from from DNA copy number and gene expression
                        data (one-sample only).
pollackCN16             Breast cancer data (copy number)
pollackGE16             Breast cancer data (gene expression)
profilesPlot            CN-GE profiles plot
rcmFit-class            Class "rcmFit" for storing the results of the
                        function RCMestimation.
rcmTest-class           Class "rcmTest" for storing the results of the
                        function RCMtest.
sigaR-package           statistics for integrative genomics analyses in
                        R
splitMatchingAtBreakpoints
                        Split matching at breakpoints
summary-method          Methods for Function summary
uniqGenomicInfo         Unique genomic location information
