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 |