annotatePeaksGenes      Annotation of peaks and genes
collateGenes            Get list of genes
countBamInGATC          Obtain region counts for BAM files
dros_counts             Example Drosophila DamID counts
geom_dm                 Plotting results from differential methylation
                        testing
geom_gatc               Plot for a GATC track
geom_genes_tx           Plotting genes
geom_peak               Plotting peaks
getGatcRegions          Extract GATC regions
identifyPeaks           Identify peaks from differentially methylated
                        regions
makeDGE                 Create DGE object for differential testing
plotCorrHeatmap         Plot correlation heatmap
plotCounts              Plot for counts for all samples across a given
                        region
plotCountsDistribution
                        Plot distribution of counts
                        'plotCountsDistribution' plots the distribution
                        of counts enabling the comparison of different
                        samples. Can highlight the different library
                        sizes of the samples.
plotCountsInPeaks       Plotting the
plotGeneOntology        Plot gene ontology results
plotWrap                Wrapper function for plotting
random_counts           Create example counts
random_edgeR_results    Create example edgeR results
random_regions          Create example regions
testDmRegions           Differential testing
testGeneOntology        Gene ontology analysis
