BuildSNNGraphLaplacians {jrSiCKLSNMF}

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 (Lun et al. 2016)

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

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<-BuildSNNGraphLaplacians(SimSickleJrSmall)