Analysis of DNA methylation data from CHARM microarrays


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Documentation for package ‘charm’ version 1.6.0

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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