filterSnapBmat: Filter bmat removing common bins and those overlapped with...

In beyondpie/pureRUtils: Commonly used R functions with pure R codes

Filter bmat removing common bins and those overlapped with blacklist

Description

Filter bmat removing common bins and those overlapped with blacklist

Usage

filterSnapBmat(
  snap = NULL,
  snapFile = NULL,
  low = 0,
  high = 0.99,
  blackListFile = NULL,
  blacklistGR = NULL,
  excludeChr = "random|chrM",
  addBmatIfEmpty = FALSE,
  binSize = 5000,
  ncores = 1
)

Arguments

snap	snap object of SnapATAC, default NULL
snapFile	characters name of the snap File to load, default NULL
low	double threshold, default 0 (bin freq <= low will be removed)
high	double threshold, default 0.99 (bin freq > high will be removed)
blackListFile	characters file of the blacklistGR, default NULL
blacklistGR	GenomicRanges object, default NULL
excludeChr	characters used to filter bmat, default "random|chrM"
addBmatIfEmpty	bool, default FALSE
binSize	integer dim of bmat, default 5,000
ncores	integer number of cores to use for parallel, default 1

Value

SnapObject

beyondpie/pureRUtils documentation built on Jan. 10, 2023, 3:22 a.m.