comma: for microbial methylation analysis

The comma package provides a complete toolkit for genome-wide analysis of bacterial DNA methylation from Oxford Nanopore sequencing data. It supports the three major modification types (6mA, 5mC, 4mC), handles input from modkit pileup (primary), Dorado BAM, and Megalodon (legacy) callers, and provides a unified data container, annotation utilities, differential methylation testing, and a full set of visualization functions.

Value

No return value. This page provides package-level documentation. See individual function pages for return values.

Main workflow

1. Load data — commaData() constructs the central commaData S4 object from per-sample methylation files.

2. QC — methylomeSummary(), coverageDepth(), plot_coverage(), plot_methylation_distribution(), and plot_pca() provide sample-level quality assessment.

3. Annotate — loadAnnotation() imports a GFF3 or BED file; annotateSites() maps methylation sites to genomic features.

4. Visualize — plot_genome_track() and plot_metagene() show methylation in a genomic context.

5. Differential methylation — diffMethyl() tests each site; results() and filterResults() extract and filter the results table; plot_volcano() and plot_heatmap() visualize the findings.

Key classes and constructors

commaData

The central S4 data container, extending SummarizedExperiment. Stores methylation (beta) and coverage matrices, per-site and per-sample metadata, genome information, genomic annotation, and motif site locations.

Package options

None. All parameters are passed directly to individual functions.

References

The modkit pileup format is documented at https://nanoporetech.github.io/modkit/.

See also

Useful links:

• https://github.com/carl-stone/CoMMA

• https://carl-stone.github.io/CoMMA/

• Report bugs at https://github.com/carl-stone/CoMMA/issues

Author

Maintainer: Carl Stone carl.j.stone@vanderbilt.edu (ORCID)