Function reference • comethyl

Package

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

Prepare Methylation Data

adjustRegionMeth(): Adjust Methylation Data for Principal Components

filterCpGs(): Filter BSseq Objects by Coverage

filterRegions(): Filter Regions

getCpGs(): Read Bismark CpG reports

getCpGtotals(): Get Total CpGs at Different Coverage Cutoffs

getDendro(): Perform Hierarchical Clustering

getPCs(): Calculate Top Principal Components

getRegionMeth(): Get Region Methylation Data

getRegionTotals(): Get Region Totals at Different Cutoffs

getRegions(): Generate Regions from CpGs

plotCpGtotals(): Visualize Total CpGs at Different Coverage Cutoffs

plotDendro(): Plot a Dendrogram

plotRegionStats(): Plot Histograms of Region Statistics

plotRegionTotals(): Visualize Region Totals at Different Cutoffs

plotSDstats(): Plot Heatmaps of Region Standard Deviation vs Features

Construct Network

getCor(): Calculate Correlations

getModuleBED(): Get a Module BED file

getModules(): Identify Modules of Comethylated Regions

getSoftPower(): Estimate Soft Power Threshold

plotHeatmap(): Plot a Heatmap with Dendrograms

plotRegionDendro(): Plot Region Dendrograms

plotSoftPower(): Plot Soft Power Fit and Connectivity

Explore Modules

annotateModule(): Annotate Module Regions

enrichModule(): Analyze Module Functional Enrichment with GREAT

getGeneList(): Extract a Gene List from Annotated Regions

getMEtraitCor(): Calculate Correlation Statistics Between Module Eigennodes and Traits

listOntologies(): Get Ontologies Available in GREAT

plotEnrichment(): Plot Functional Enrichment Results

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

Test Module Preservation

getModulePreservation(): Calculate Module Preservation

plotModulePreservation(): Visualize Module Preservation