Function reference • DMRichR

Main function

DM.R(): Run the pipeline

Preprocessing

processBismark(): Preprocess cytosine reports

Annotations

annotationDatabases(): Load annotation databases

annotateRegions(): Annotate DMRs and blocks

DMReport(): Create an html report of DMRs or blocks

getCpGs(): Obtain CpG island, CpG shore, CpG shelf, and open sea annotations

getExons(): Obtain exons for plotting

DMR plots

plotDMRs2(): Plot Differentially Methylated Regions

smoothPheatmap(): DMR heatmap

Manhattan(): Manhattan plot

Global methylation

Statistics

globalStats(): Test for global methylation differences

Value extraction

CGi(): Extract methylation values from CpG islands

CpGs(): Extract single CpG methylation values

windows(): Extract methylation values from tiled genomic windows

Plots

PCA(): PCA plot of extracted methylation values

densityPlot(): Density plot of extracted methylation values

Enrichment testing

Gene ontology

GOfuncR(): GOfuncR gene ontology enrichment testing

slimGO(): Slim GO results

GOplot(): Plot slimmed GO results

Gene region and CpG

DMRichCpG(): CpG annotation enrichment testing

DMRichGenic(): Gene region enrichment testing

DMRichPlot(): Plot gene region and CpG annotation enrichment testing

DMparseR(): Combined plot of stratified gene region and CpG annotation enrichment testing

Imprinting

imprintOverlap(): Imprinted gene enrichment testing

Reference epigenomics

chromHMM(): Chromatin state enrichments

chromHMM_heatmap(): Chromatin state heatmap

roadmap(): Chromatin mark enrichments

roadmap_heatmap(): Chromatin mark heatmap

Transcription factor motifs

prepareHOMER(): Save regions for HOMER

HOMER(): Transcription factor motif analysis

Machine learning

methylLearn(): Machine learning feature selection

Helper functions

arrayLift(): LiftOver Infinium array probe IDs to hg38 coordinates

dmrList(): Stratify DMRs by directionality

extend(): Extend genomic ranges

getBackground(): bsseq style background regions

gg_color_hue(): ggplot2 colors

gr2bed(): Save a genomic ranges object as a bed file

read_excel_all(): Read entire excel document

smooth2txt(): Save regions and methylation values

Package

DMRichR: DMRichR

.onAttach(): onAttach