Damsel: an end to end analysis of DamID
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Documentation for package ‘Damsel’ version 1.2.0
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 |