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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("charm")
AuthorMartin Aryee, Peter Murakami, Harris Jaffee, Rafael Irizarry
Bioconductor views DNAMethylation Microarray
Date of publicationNone
MaintainerPeter Murakami <pmurakam@jhu.edu>
LicenseLGPL (>= 2)
Version2.22.0

View on Bioconductor

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...

Functions

bgAdjust Man page
clusterMaker Man page
cmdsplot Man page
controlQC Man page
countGC Man page
cpgdensity Man page
dmrFdr Man page
dmrFind Man page
dmrFinder Man page
dmrPlot Man page
getControlIndex Man page
maxDensity Man page
methp Man page
methPercent Man page
normalizeBetweenSamples Man page
normalizeWithinSamples Man page
plotDensity Man page
plotDMRs Man page
plotRegions Man page
pmQuality Man page
qcReport Man page
qval Man page
readCharm Man page
regionMatch Man page
regionPlot Man page
spatialAdjust Man page
validatePd Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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