# Damsel: an end to end analysis of DamID

## Documentation for package ‘Damsel’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
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