Export methylation data as a BED file

Writes per-site methylation beta values for a single sample from a commaData object to a 9-column BED file (BED9 format), suitable for visualisation in IGV, UCSC Genome Browser, or other genome browsers that support the itemRGB field.

Usage

writeBED(
  object,
  file,
  sample,
  mod_type = NULL,
  rgb_scale = TRUE,
  track_name = sample,
  track_description = "methylation beta values"
)

Arguments

object: A commaData object.
file: Character string. Path to the output BED file. The file will be created or overwritten.
sample: Character string. Name of the sample to export. Must match a column name in methylation(object).
mod_type: Character string or NULL. If provided, only sites of the specified modification type are written (e.g., "6mA"). If NULL (default), all sites are written.
rgb_scale: Logical. If TRUE (default), an itemRGB column is added based on the methylation score using a blue-to-red gradient (low = blue, high = red). If FALSE, itemRGB is set to "0,0,0" for all sites.
track_name: Character string. Name shown in the genome browser track header. Defaults to sample.
track_description: Character string. Description shown in the track header. Defaults to "methylation beta values".

Value

Invisibly returns the path to the written file (file).

Details

The BED score field (column 5) contains the beta value multiplied by 1000 and rounded to the nearest integer (range 0–1000), which is the standard convention for methylation BED files. The itemRGB colour gradient transitions as follows: score ≤ 200 = blue (0,0,255), score ≤ 400 = blue-purple (83,0,172), score ≤ 600 = purple (167,0,85), score ≤ 800 = red-purple (222,0,28), score ≤ 1000 = red (250,0,0).

Sites with NA methylation (below the coverage threshold) are excluded from the output.

Examples

data(comma_example_data)
tmp <- tempfile(fileext = ".bed")
writeBED(comma_example_data, file = tmp, sample = "ctrl_1", mod_type = "6mA")

# \donttest{
# Write to a permanent file
writeBED(comma_example_data,
         file    = "ctrl_1_methylation.bed",
         sample  = "ctrl_1",
         mod_type = "6mA")
# }