Package index • comma

All functions

annotateSites(): Annotate methylation sites relative to genomic features
annotation(<commaData>): Accessor for genomic feature annotation
comma-package comma: comma: for microbial methylation analysis
commaData-class: commaData: the central data object for the comma package
commaData(): Create a commaData object from methylation calling output files
comma_example_data: Synthetic example methylation dataset for the comma package
coverage(<commaData>): Accessor for the sequencing coverage (read depth) matrix
coverageDepth(): Windowed sequencing depth across the genome
diffMethyl(): Identify differentially methylated sites between conditions
filterResults(): Filter differential methylation results by significance thresholds
findMotifSites(): Find all instances of a sequence motif in a genome
genome(<commaData>): Accessor for genome size information
loadAnnotation(): Load genomic feature annotations from a GFF3 or BED file
methylation(): Accessor for the methylation (beta value) matrix
methylomeSummary(): Summarize per-sample methylation and coverage distributions
modTypes(): Return the modification types present in a commaData object
motifSites(): Accessor for motif site positions
plot_coverage(): Plot coverage depth distribution
plot_genome_track(): Genome browser–style methylation track plot
plot_heatmap(): Heatmap of top differentially methylated sites
plot_metagene(): Metagene plot of methylation across genomic features
plot_methylation_distribution(): Plot methylation beta value distributions
plot_pca(): PCA of methylation profiles
plot_volcano(): Volcano plot for differential methylation results
results(): Extract differential methylation results as a tidy data frame
sampleInfo(): Accessor for per-sample metadata
siteInfo(): Accessor for per-site metadata
slidingWindow(): Sliding window methylation summary along the genome
`[`(<commaData>,<ANY>,<ANY>,<ANY>): Subset a commaData object by sites and/or samples
subset(): Subset a commaData object by condition, modification type, or chromosome
varianceByDepth(): Methylation variance as a function of sequencing depth
writeBED(): Export methylation data as a BED file