call_peaks_macs: MACS peak calling

In Bankso/SCAR: SpLiT-ChEC analysis with R

MACS peak calling

Description

MACS peak calling

Usage

call_peaks_macs(
  SCAR_obj,
  outdir = getwd(),
  process = "callpeak",
  in_form = NA,
  genome_size = NA,
  tag_size = NA,
  width = NA,
  mfold = NA,
  q_val = NA,
  p_val = NA,
  broad = FALSE
)

Arguments

SCAR_obj	SCAR object.
outdir	Output directory.
process	Name of the MACS function you want, def. is 'callpeaks'
in_form	Format of input, default is to auto-determine
genome_size	Size of mappable genome
tag_size	size of adaptors, default is to auto-determine
width	Width to use for model building scan, optional
mfold	upper and lower limit for model building, optional
q_val	min q value/FDR cutoff, optional
p_val	Set p val instead of q, optional
broad	Peaks are expected to be broad, TRUE or FALSE, default=FALSE

Bankso/SCAR documentation built on Aug. 20, 2022, 5:26 a.m.