Man pages for charm
Analysis of DNA methylation data from CHARM microarrays

bgAdjustRemove background
clusterMakerRedefine array regions given chromosomal coordinates.
cmdsplotClassical multi-dimensional scaling plot of charm data.
controlQCBoxplots of control and non-control probes
countGCCount probe GC content
cpgdensityGet CpG density for genomic regions
dmrFdrCalculate FDR q-values for differentially methylated regions...
dmrFindIdentify DMR candidates using a regression-based approach and...
dmrFinderFind differentially methylated regions (DMRs)
dmrPlotPlot differentially methylated regions (DMRs) found using the...
getControlIndexGet indices of control probes from CpG-free regions
maxDensityFind the mode of a density function
methpEstimate DNA methylation
methPercentEstimate percentage DNA methylation from log-ratios
normalizeBetweenSamplesBetween-sample normalization
normalizeWithinSamplesWithin-sample normalization for two-color data
plotDensityLog-ratio density plot for all probes and control probes
plotDMRsPlot differentially methylated regions (DMRs) found using the...
plotRegionsPlot user-provided regions.
pmQualityCalculate probe quality scores
qcReportMicroarray quality report
qvalObtain False Discovery Rate q-values for the DMR candidates...
readCharmRead in McrBC/CHARM DNA methylation microarray data
regionMatchGiven two data frames with columns "chr", "start", and "end",...
regionPlotPlot user-supplied genomic regions using data returned by the...
spatialAdjustCorrect spatial artifacts
validatePdValidate a sample description file for two-color microarray...
charm documentation built on May 6, 2019, 2:29 a.m.