bgAdjust                Remove background
clusterMaker            Redefine array regions given chromosomal
                        coordinates.
cmdsplot                Classical multi-dimensional scaling plot of
                        charm data.
controlQC               Boxplots of control and non-control probes
countGC                 Count probe GC content
cpgdensity              Get CpG density for genomic regions
dmrFdr                  Calculate FDR q-values for differentially
                        methylated regions (DMRs)
dmrFind                 Identify DMR candidates using a
                        regression-based approach and correcting for
                        batch effects.
dmrFinder               Find differentially methylated regions (DMRs)
dmrPlot                 Plot differentially methylated regions (DMRs)
                        found using the dmrFinder function.
getControlIndex         Get indices of control probes from CpG-free
                        regions
maxDensity              Find the mode of a density function
methPercent             Estimate percentage DNA methylation from
                        log-ratios
methp                   Estimate DNA methylation
normalizeBetweenSamples
                        Between-sample normalization
normalizeWithinSamples
                        Within-sample normalization for two-color data
plotDMRs                Plot differentially methylated regions (DMRs)
                        found using the dmrFind function.
plotDensity             Log-ratio density plot for all probes and
                        control probes
plotRegions             Plot user-provided regions.
pmQuality               Calculate probe quality scores
qcReport                Microarray quality report
qval                    Obtain False Discovery Rate q-values for the
                        DMR candidates returned by dmrFind.
readCharm               Read in McrBC/CHARM DNA methylation microarray
                        data
regionMatch             Given two data frames with columns "chr",
                        "start", and "end", identify the nearest region
                        in one to the other.
regionPlot              Plot user-supplied genomic regions using data
                        returned by the dmrFinder function.
spatialAdjust           Correct spatial artifacts
validatePd              Validate a sample description file for
                        two-color microarray data
