# Damsel: an end to end analysis of DamID

## Documentation for package ‘Damsel’ version 1.8.0

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

## 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
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