charm: Analysis of DNA methylation data from CHARM microarrays

This package implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. It finds differentially methylated regions between samples, calculates percentage methylation estimates and includes array quality assessment tools.

AuthorMartin Aryee, Peter Murakami, Harris Jaffee, Rafael Irizarry
Date of publicationNone
MaintainerPeter Murakami <>
LicenseLGPL (>= 2)

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Man 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...

dmrFind: Identify DMR candidates using a regression-based approach and...

dmrFinder: Find differentially methylated regions (DMRs)

dmrPlot: Plot differentially methylated regions (DMRs) found using the...

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...

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...

readCharm: Read in McrBC/CHARM DNA methylation microarray data

regionMatch: Given two data frames with columns "chr", "start", and "end",...

regionPlot: Plot user-supplied genomic regions using data returned by the...

spatialAdjust: Correct spatial artifacts

validatePd: Validate a sample description file for two-color microarray...

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