landmarkEmbedding: SnapATAC landmark embedding.

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

SnapATAC landmark embedding.

Description

SnapATAC landmark embedding.

Usage

landmarkEmbedding(
  snap = NULL,
  snapFile = NULL,
  blacklistGR = NULL,
  blackListFile = NULL,
  binSize = 5000,
  nPC = 50,
  ncores = 1,
  outFile = NULL,
  excludeChr = "random|chrM",
  removeBmat = FALSE,
  removeJmat = FALSE
)

Arguments

snap	snap object of SnapATAC, default NULL
snapFile	characters name of the snap File to load, default NULL
blacklistGR	GenomicRanges object, default NULL
blackListFile	characters file of the blacklistGR, default NULL
binSize	integer dim of bmat, default 5,000
nPC	integer dim of embeding for embedding, default 50
ncores	integer number of cores to use for parallel, default 1
outFile	characters to which we write snap with embedding, default NULL
excludeChr	characters used to filter bmat, default "random|chrM"
removeBmat	bool default FALSE
removeJmat	bool default FALSE

Value

SnapObject

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