SnapATAC_runDiffusionMaps: Core of DiffusionMaps for landmark cells.

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

Core of DiffusionMaps for landmark cells.

Description

Core of DiffusionMaps for landmark cells.

Usage

SnapATAC_runDiffusionMaps(bmat, nPC = 30, n = 1000, outlier = 0.999)

Arguments

bmat	sparse Matrix, cell by feature, after binarization
nPC	integer, default is 30
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

Value

list of five elements

• dmat dense matrix, cell by features

• sdev vector, standard deviation

• cutoff numeric, cutoff of outiliers for the normalized Jaccard similarity matrix

• betas numeric vector of three elements, regression coefficients for reducing the random depth effect in Jaccard similarity matrix.

• diagFactor Diagonal Matrix, inverse of square root of the rowSums of normalized Jaccard similarity matrix.

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