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