runMACS: Call Peaks Using MACS2

In r3fang/SnapATAC: Single Nucleus Analysis Package for ATAC-Seq

Call Peaks Using MACS2

Description

Identify peaks using selected cells. Fragments belonging to a subset of cells are extracted and used to identify peaks using MACS2. This function requires "MACS2" and "snaptools" preinstalled and excutable.

Usage

runMACS(obj, output.prefix, path.to.snaptools, path.to.macs, gsize, tmp.folder,
  buffer.size = 500,
  macs.options = "--nomodel --shift 37 --ext 73 --qval 1e-2 -B --SPMR --call-summits",
  num.cores = 1, keep.minimal = TRUE)

Arguments

obj	A snap object.
output.prefix	Prefix of output file which will be used to generate output file names.
path.to.snaptools	Path to snaptools excutable file.
path.to.macs	Path to macs2 excutable file.
gsize	effective genome size. 'hs' for human, 'mm' for mouse, 'ce' for C. elegans, 'dm' for fruitfly (default: None)
tmp.folder	Directory to store temporary files generated by runMACS.
buffer.size	Buffer size for incrementally increasing internal array size to store reads alignment information. In most cases, you don't have to change this parameter. However, if there are very high coverage dataset that each barcode has more than 10000 fragments, it's recommended to specify a smaller buffer size in order to decrease memory usage (but it will take longer time to read snap files) [1000].
macs.options	String indicate options you would like passed to macs2. strongly do not recommand to change unless you know what you are doing. the default is '–nomodel –shift 37 –ext 73 –qval 1e-2 -B –SPMR –call-summits'.
num.cores	Number of cores to use for omputing [1].
keep.minimal	Keep minimal version of output [TRUE].

Value

Return a data.frame object that contains the peak information

r3fang/SnapATAC documentation built on March 29, 2022, 4:33 p.m.