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| 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 |
| maxDensity | Find the mode of a density function |
| methp | Estimate DNA methylation |
| methPercent | Estimate percentage DNA methylation from log-ratios |
| 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 |