computeCellSim: Compute Cell Similarity

In PFPrzytycki/CellWalkR: An R Package for Integrating and Visualizing Single-Cell and Bulk Data to Resolve Regulatory Elements

Compute Cell Similarity

Description

computeCellSim computes a cell-to-cell similarity matrix using the given method. Currently only Jaccard similarity is implemented.

Usage

computeCellSim(ATACMat, method = sparseJaccard)

Arguments

ATACMat	either a cell-by-peak matrix, a SnapATAC object, an ArchR project, or a Cicero count table
method	function, the method used to compute cell similarity, should operate on rows of a matrix. The default is Jaccard similiarty, but a second built in option is PCAdist which computes the euclidean distance in PCA space

Value

matrix of cell-to-cell similarity

Examples

data("SampleCellWalkRData")
computeCellSim(SampleCellWalkRData$ATACMat)

PFPrzytycki/CellWalkR documentation built on Oct. 26, 2023, 1:50 p.m.