Man pages for cemordaunt/comethyl
An R Package for Weighted Region Comethylation Network Analysis
| adjustRegionMeth | Adjust Methylation Data for Principal Components |
| annotateModule | Annotate Module Regions |
| comethyl | comethyl: An R package for weighted region comethylation... |
| enrichModule | Analyze Module Functional Enrichment with GREAT |
| filterCpGs | Filter BSseq Objects by Coverage |
| filterRegions | Filter Regions |
| getCor | Calculate Correlations |
| getCpGs | Read Bismark CpG reports |
| getCpGtotals | Get Total CpGs at Different Coverage Cutoffs |
| getDendro | Perform Hierarchical Clustering |
| getGeneList | Extract a Gene List from Annotated Regions |
| getMEtraitCor | Calculate Correlation Statistics Between Module Eigennodes... |
| getModuleBED | Get a Module BED file |
| getModulePreservation | Calculate Module Preservation |
| getModules | Identify Modules of Comethylated Regions |
| getPCs | Calculate Top Principal Components |
| getRegionMeth | Get Region Methylation Data |
| getRegions | Generate Regions from CpGs |
| getRegionTotals | Get Region Totals at Different Cutoffs |
| getSoftPower | Estimate Soft Power Threshold |
| listOntologies | Get Ontologies Available in GREAT |
| plotCpGtotals | Visualize Total CpGs at Different Coverage Cutoffs |
| plotDendro | Plot a Dendrogram |
| plotEnrichment | Plot Functional Enrichment Results |
| plotHeatmap | Plot a Heatmap with Dendrograms |
| plotMethTrait | Plot Module Methylation Values By a Sample Trait |
| plotMEtraitCor | Plot a Heatmap of Correlations Between Module Eigennodes and... |
| plotMEtraitDot | Visualize a Module Eigennode - Trait Correlation as a Dot... |
| plotMEtraitScatter | Visualize a Module Eigennode - Trait Correlation as a Scatter... |
| plotModulePreservation | Visualize Module Preservation |
| plotRegionDendro | Plot Region Dendrograms |
| plotRegionStats | Plot Histograms of Region Statistics |
| plotRegionTotals | Visualize Region Totals at Different Cutoffs |
| plotSDstats | Plot Heatmaps of Region Standard Deviation vs Features |
| plotSoftPower | Plot Soft Power Fit and Connectivity |
