charm: Analysis of DNA methylation data from CHARM microarrays

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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.

Author
Martin Aryee, Peter Murakami, Harris Jaffee, Rafael Irizarry
Date of publication
None
Maintainer
Peter Murakami <pmurakam@jhu.edu>
License
LGPL (>= 2)
Version
2.20.0

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...

Files in this package

charm/CHANGES
charm/DESCRIPTION
charm/NAMESPACE
charm/R
charm/R/charm.R
charm/R/deprecated.R
charm/R/dmrPlotting.R
charm/R/pipeline1.R
charm/build
charm/build/vignette.rds
charm/inst
charm/inst/CITATION
charm/inst/NEWS
charm/inst/doc
charm/inst/doc/charm.R
charm/inst/doc/charm.Rnw
charm/inst/doc/charm.pdf
charm/man
charm/man/bgAdjust.Rd
charm/man/clusterMaker.Rd
charm/man/cmdsplot.Rd
charm/man/controlQC.Rd
charm/man/countGC.Rd
charm/man/cpgdensity.Rd
charm/man/dmrFdr.Rd
charm/man/dmrFind.Rd
charm/man/dmrFinder.Rd
charm/man/dmrPlot.Rd
charm/man/getControlIndex.Rd
charm/man/maxDensity.Rd
charm/man/methPercent.Rd
charm/man/methp.Rd
charm/man/normalizeBetweenSamples.Rd
charm/man/normalizeWithinSamples.Rd
charm/man/plotDMRs.Rd
charm/man/plotDensity.Rd
charm/man/plotRegions.Rd
charm/man/pmQuality.Rd
charm/man/qcReport.Rd
charm/man/qval.Rd
charm/man/readCharm.Rd
charm/man/regionMatch.Rd
charm/man/regionPlot.Rd
charm/man/spatialAdjust.Rd
charm/man/validatePd.Rd
charm/vignettes
charm/vignettes/charm.Rnw
charm/vignettes/charmVignette.bib