Calling MACS2 peak caller and merging resulting peaks

Source: R/peak_calling.R

Calling MACS2 peak caller and merging resulting peaks

call_macs2_merge_peaks(
  affectation,
  odir,
  p.value,
  format = c("scBED", "BAM")[1],
  ref,
  peak_distance_to_merge
)

Arguments

affectation

Annotation data.frame with cell cluster and cell id information
odir

Output directory to write MACS2 output
p.value

P value to detect peaks, passed to MACS2
format

File format, either "BAM" or "scBED"
ref

Reference genome to get chromosome information from.
peak_distance_to_merge

Distance to merge peaks

Value

A list of merged GRanges peaks