bgAdjust                Remove background
countGC                 Count probe GC content
cpgdensity              Get CpG density for genomic regions
dmrFdr                  Calculate FDR q-values for differentially
                        methylated regions (DMRs)
dmrFinder               Find differentially methylated regions (DMRs)
dmrPlot                 Plot differentially methylated regions (DMRs)
getControlIndex         Get indices of control probes from CpG-free
                        regions
methPercent             Estimate percentage DNA methylation from
                        log-ratios
methp                   Estimate DNA methylation
normalizeBetweenSamples
                        Between-sample normalization
normalizeWithinSamples
                        Within-sample normalization for two-color data
plotDensity             Log-ratio density plot for all probes and
                        control probes
qcReport                Microarray quality report
readCharm               Read in McrBC/CHARM DNA methylation microarray
                        data
regionPlot              Plot user-supplied genomic regions.
spatialAdjust           Correct spatial artifacts
validatePd              Validate a sample description file for
                        two-color microarray data
