BuildKNNGraphLaplacians {jrSiCKLSNMF}

Build KNN graphs and generate their graph Laplacians

Description

Generate graph Laplacians for graph regularization of jrSiCKLSNMF from the list of raw count matrices using a KNN graph. Note that this is only appropriate when the number of features is considerably greater than the number of cells in all modalities. If this is not the case, please use BuildSNNGraphLaplacians or any other method of graph construction that does not rely on the Euclidean distance and store the graph Laplacians for each modality as a list in the graph.laplacian.list slot.

Usage

BuildKNNGraphLaplacians(SickleJr, k = 20)

Arguments

SickleJr

An object of class SickleJr

k

Number of KNN neighbors to calculate; by default, is set to 20

Value

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

References

Lun AT, McCarthy DJ, Marioni JC (2016). “A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.” F1000Research, 5. ISSN 1759796X, doi:10.12688/F1000RESEARCH.9501.2/DOI, https://pubmed.ncbi.nlm.nih.gov/27909575/.

Examples

SimSickleJrSmall<-BuildKNNGraphLaplacians(SimSickleJrSmall)