# Analysis of DNA methylation data from CHARM microarrays

## Documentation for package ‘charm’ version 2.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
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
plotDMRs | Plot differentially methylated regions (DMRs) found using the dmrFind function.
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