AnalysisRegionResults   AnalysisRegionResults instances
AnalysisResults         AnalysisResults instances
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
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.
filterSet               Filter a 'MethylationSet', an 'ExpressionSet'
                        or a 'SnpSet'
getGeneVals             Get all probes related to gene
normalSNP               Normalize SNPs values
plotBestFeatures        Plot best n cpgs
plotEWAS                Plot a Manhattan plot with the probe results
plotFeature             Plot values of a feature
plotLM                  Plot a vector of R2
plotQQ                  QQ plot of probe analysis
plotRDA                 Plot RDA results
plotRegion              Plot of the region
plotRegionR2            Plot R2 region values
plotVolcano             Make a Volcano plot with the probe results
prepareMethylationSet   Generating a 'MethylationSet'
preparePhenotype        Process a table of phenotypes
topRDAhits              Get the top features associated with the RDA
