Parse a modkit pileup BED file into a tidy per-site data frame

Reads a single-sample modkit pileup output file and returns a tidy data frame of per-site methylation values. This is an internal function called by commaData.

Usage

.parseModkit(file, sample_name, mod_type = NULL, min_coverage = 5L)

Arguments

file

Character string. Path to the modkit pileup BED file.

sample_name

Character string. Name for this sample (used in messages only; not added to the returned data frame).

mod_type

Character vector or NULL. If provided, only sites with a matching modification type (e.g., "6mA", "5mC", "4mC") are returned. NULL retains all modification types.

min_coverage

Integer. Minimum read depth required to retain a site. Sites with coverage < min_coverage are dropped. Default 5.

Value

A data.frame with columns:

chrom

Chromosome name (character).

position

1-based genomic position (integer).

strand

Strand, "+" or "-" (character).

mod_type

Modification type: "6mA", "5mC", or "4mC" (character).

beta

Proportion of reads called methylated, range 0–1 (numeric).

coverage

Total read depth at this site (integer).