callACRs: callACRs

In plantformatics/Socrates: Analysis of scATAC-seq data

callACRs

Description

This function calls ACRs using the bulk Tn5 integration sites with MACS2

Usage

callACRs(
  obj,
  genomesize = 1.6e+09,
  shift = -50,
  extsize = 100,
  output = "bulk_peaks",
  tempdir = "./macs2_temp",
  verbose = T,
  fdr = 0.05
)

Arguments

obj	Object output from loadBEDandGenomeData. Required.
genomesize	Effective genome size parameter for MACS2 (defaults to 1.6e9 for Zea mays).
shift	Shift the start coordinates upstream. Defaults to -50 bp.
extsize	Extends the fragment length downstream. Defaults to 100 bp.
output	Output file names for MACS2. Defaults to 'bulk_peaks'.
tempdir	Directory name to store the output of MACS2. Defaults to "./macs2_temp".
verbose	Logical. Whether to print information.
fdr	Float. Significance cut-off for peak calling. Defaults to q-value 0.05.

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.