SnapATAC_DiffusionMaps: DiffusionMaps method in SnapATAC

In beyondpie/smmtools: Single-cell multi-omics sequenceing data tools

DiffusionMaps method in SnapATAC

Description

DiffusionMaps method in SnapATAC

Usage

SnapATAC_DiffusionMaps(
  bmatSnap,
  nLandmark = 10000,
  n = 1000,
  outlier = 0.999,
  nPC = 30,
  seed = 1
)

Arguments

bmatSnap	sparse matrix, cell by feature
nLandmark	integer, numebr of landmark cells, default is 10,000
n	integer, used for fitting regression of random depth effect, default is 1000
outlier	double, used for choosing threshold of normalized Jaccard similarity matrix, default is 0.999
nPC	integer, default is 30
seed	integer, default is 1

Value

list of two element

• dmat dense matrix, cell by principle components, keep the same order of cells

• sdev vector, length of principle components

beyondpie/smmtools documentation built on July 1, 2022, 4:33 a.m.