Metagene plot of methylation across genomic features

Computes average methylation beta values at normalized positions across genomic features (e.g., genes from TSS to TTS) and plots the smoothed profile. Useful for assessing whether methylation is enriched at particular positions within a feature class.

Usage

plot_metagene(object, feature = "gene", mod_type = NULL, n_bins = 50L)

Arguments

object

A commaData object with a non-empty annotation slot or a user-supplied features GRanges.

feature

Character string specifying the feature type to use as the reference. Must match a value in the feature_type metadata column of the annotation. Default "gene".

mod_type

Character string specifying a single modification type (e.g., "6mA", "5mC"). If NULL (default), all modification types are used.

n_bins

Positive integer. Number of equal-width bins to divide the normalized feature position \([0, 1]\) into. Default 50.

Value

A ggplot object. The x-axis shows normalized position within the feature (0 = TSS, 0.5 = midpoint, 1 = TTS); the y-axis shows mean methylation (beta). One line is drawn per sample, colored by sample name. Dashed vertical lines mark the TSS (0) and TTS (1).

Details

Internally calls annotateSites(type = "metagene") to compute normalized positions (0 = TSS, 1 = TTS) for each methylation site that overlaps a feature of the requested type. Sites that do not overlap any feature are excluded from the plot. The mean beta value is then computed within each position bin for each sample.

See also

annotateSites, plot_genome_track

Examples

data(comma_example_data)
plot_metagene(comma_example_data, feature = "gene")


# Only 6mA sites
plot_metagene(comma_example_data, feature = "gene", mod_type = "6mA")