Analysis of DNA methylation data from CHARM microarrays


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Documentation for package ‘charm’ version 2.18.0

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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