Package index • comethyl

Package

comethyl: comethyl: An R package for weighted region comethylation network analysis

Prepare Methylation Data

getCpGs(): Read Bismark CpG reports
getCpGtotals(): Get Total CpGs at Different Coverage Cutoffs
plotCpGtotals(): Visualize Total CpGs at Different Coverage Cutoffs
filterCpGs(): Filter BSseq Objects by Coverage
getRegions(): Generate Regions from CpGs
getRegionTotals(): Get Region Totals at Different Cutoffs
plotRegionTotals(): Visualize Region Totals at Different Cutoffs
getRegionMeth(): Get Region Methylation Data
filterRegions(): Filter Regions
plotRegionStats(): Plot Histograms of Region Statistics
plotSDstats(): Plot Heatmaps of Region Standard Deviation vs Features
getDendro(): Perform Hierarchical Clustering
plotDendro(): Plot a Dendrogram
getPCs(): Calculate Top Principal Components
adjustRegionMeth(): Adjust Methylation Data for Principal Components

Construct Network

getCor(): Calculate Correlations
getSoftPower(): Estimate Soft Power Threshold
plotSoftPower(): Plot Soft Power Fit and Connectivity
getModules(): Identify Modules of Comethylated Regions
plotRegionDendro(): Plot Region Dendrograms
plotHeatmap(): Plot a Heatmap with Dendrograms
getModuleBED(): Get a Module BED file

Explore Modules

getMEtraitCor(): Calculate Correlation Statistics Between Module Eigennodes and Traits
plotMEtraitCor(): Plot a Heatmap of Correlations Between Module Eigennodes and Traits
plotMEtraitDot(): Visualize a Module Eigennode - Trait Correlation as a Dot Plot
plotMEtraitScatter(): Visualize a Module Eigennode - Trait Correlation as a Scatter Plot
plotMethTrait(): Plot Module Methylation Values By a Sample Trait
annotateModule(): Annotate Module Regions
getGeneList(): Extract a Gene List from Annotated Regions
enrichModule(): Analyze Module Functional Enrichment with GREAT
listOntologies(): Get Ontologies Available in GREAT
plotEnrichment(): Plot Functional Enrichment Results

Test Module Preservation

getModulePreservation(): Calculate Module Preservation
plotModulePreservation(): Visualize Module Preservation