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 <email@example.com>|
|License||LGPL (>= 2)|
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...