BuildSNNGraphLaplacians: Build SNN graphs and generate their graph Laplacians

In jrSiCKLSNMF: Multimodal Single-Cell Omics Dimensionality Reduction

Build SNN graphs and generate their graph Laplacians

Description

Generate graph Laplacians for graph regularization of jrSiCKLSNMF from the list of raw count matrices using an SNN graph. SNN is more robust to situations where the number of cells outnumbers the number of features. Uses the scran package's BuildSNNGraph function \insertCiteLun2016jrSiCKLSNMF

Usage

BuildSNNGraphLaplacians(SickleJr, k = 20)

Arguments

SickleJr	An object of class SickleJr
k	Number of KNN neighbors to calculate SNN graph; defaults to 20

Value

An object of class SickleJr with list of graph Laplacians in sparse matrix format added to its graph.laplacian.list slot

References

\insertRef

Lun2016jrSiCKLSNMF

Examples

SimSickleJrSmall<-BuildSNNGraphLaplacians(SimSickleJrSmall)

jrSiCKLSNMF documentation built on Aug. 12, 2025, 1:08 a.m.