runSnapAddPmat: Add cell-by-peak matrix to a snap file

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

Add cell-by-peak matrix to a snap file

Description

This function takes a peak list and a snap object as input and add cell-by-peak matrix into the existing snap file.

Usage

runSnapAddPmat(obj, peak, path.to.snaptools, tmp.folder, num.cores, buffer.size)

Arguments

obj	A snap obj.
peak	A GenomicRanges object that contains peak coordinates.
path.to.snaptools	Path to snaptools excutable file.
tmp.folder	Directory to store temporary files generated by this program.
num.cores	Number of CPUs to use.
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].

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