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) |
getControlIndex | Get indices of control probes from CpG-free regions |
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 |
spatialAdjust | Correct spatial artifacts |
validatePd | Validate a sample description file for two-color microarray data |