DAPipeline              Perform differential methylation analysis
DAProbe                 Perform per probe analysis
DARegion                Detect regions differentially methylated
DARegionAnalysis        Analyse methylation or expression in a specific
                        range
MEAL                    MEAL (Methylation and Expression AnaLizer):
                        Package for analysing methylation and
                        expression data
MEAL-defunct            Defunct functions
RDAset                  Calculate RDA for a set
analysisRegionResults   Old class to encapsulate results (deprecated in
                        new version)
analysisResults         Old class to encapsulate results (deprecated in
                        new version)
calculateRelevantSNPs   Calculate the SNPs correlated to cpgs
computeRDAR2            Compute signification of RDA test
correlationMethExprs    Computes the correlation between methylation
                        and expression
correlationMethSNPs     Computes the correlation between methylation
                        and SNPs
createRanges            Create 'GenomicRanges' from data.frame
explainedVariance       Calculate R2 for different variables
exportResults           Exports results data.frames to csv files.
filterResults           Filter the data.frame obtained from probe
                        analysis
filterSet               Filter a 'MethylationSet', an 'ExpressionSet'
                        or a 'SnpSet'
getGeneVals             Get all probes related to a gene
getProbeResults         Obtain probe results from a 'ResultSet'
getRDAresults           Get a summary of RDA results
normalSNP               Normalize SNPs values
plotBestFeatures        Plot best n cpgs
plotFeature             Plot values of a feature
plotLM                  Plot a vector of R2
plotRDA                 Plot RDA results
plotRegion              Plot results in a genomic region
prepareMethylationSet   Generating a 'MethylationSet'
preparePhenotype        Process a table of phenotypes
runBlockFinder          Run blockFinder
runBumphunter           Run bumphunter
runDMRcate              Run DMRcate
runDiffMeanAnalysis     Run differential mean analysis
runDiffVarAnalysis      Run differential variance analysis
runPipeline             Perform differential methylation analysis
runRDA                  Calculate RDA for a set
runRegionAnalysis       Run different DMR detection methods
topRDAhits              Get the top features associated with the RDA
