Man pages for Shicheng-Guo/edmr
Empirical differentially methylated regions calculation
| ACF | Auto correlation function |
| cpgi.anno | generate CpG islands GRangesList object |
| dist_to_mixmdl | Distance to mixmdl |
| edmr | Empirical differentially methylated regions |
| eDMR.sub | edmr sub function |
| filter.dmr | significant DMRs |
| genebody.anno | generate genebody GRangesList object |
| get.break_point | get break point to minimize the cost function. |
| getCorr | Auto correlation function |
| get.dist.cutoff | get distance cutoff from 'mixtools' object |
| getDMR | Calculate the p-value for the differentially methylated... |
| get.dmr.genes | get gene list based the genebody granges |
| get.hyper.dmr | get hyper-methylated DMRs |
| get.hypo.dmr | get hypo-methylated DMRs |
| getPeaks | Calculate emprical raw regions from 'myDiff' object. |
| myDiffToDMR | calculate differentially methylated regions from 'myDiff'... |
| myDiff.to.mixmdl | obtain mixtools model from 'myDiff' object |
| plotCost | plot cost function and the determined distance cutoff |
| plot.dmr.distr | plot eDMR distribution over the subject genomic ranges |
| plotMdl1 | plot the fitted bimodal normal distribution for CpGs... |
| readTableFast | Read text file fast by predicting and feeding 'colClass'... |
| stouffer | Stouffer test |
| stouffer.liptak | Stoffer Liptak test |
