runMACSForAll: Call Peaks Using MACS2 For All Clusters

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

Call Peaks Using MACS2 For All Clusters

Description

Identify peaks for all clusters. Fragments belonging to each subset or cluster of cells are extracted and used to identify peaks using MACS2. This function requires "MACS2" and "snaptools" preinstalled and excutable.

Usage

runMACSForAll(obj, output.prefix, path.to.snaptools, path.to.macs, gsize,
  tmp.folder, num.cores = 1, min.cells = 100, buffer.size = 500,
  macs.options = "--nomodel --shift 37 --ext 73 --qval 1e-2 -B --SPMR --call-summits",
  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 runMACSForAll.
num.cores	number of cpus to use [1].
min.cells	min number of cells to perform peak calling [100]. Clusters with cells less than num.cells will be excluded.
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'.
keep.minimal	Keep minimal version of output [TRUE].

Value

Return a GRanges object that contains the non-overlapping combined peaks

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