Enrichment scoring of gene sets on expression data

Performs single-sample enrichment scoring using GSVA or AUCell. When AUCell is specified, output values reflect the AUC levels scaled by 100 and log2 transformed.

Usage

runScoreGeneSets(K2res, ScoreGeneSetMethod = NULL, useCors = NULL)

Arguments

ScoreGeneSetMethod

Character. Method for gene set scoring. Use one of either 'GSVA' (default) or 'AUCELL'.

useCors

Numeric. Number of cores to use for parallelizable processes.

Value

An object of class K2.

References

Reed ER, Monti S (2021). “Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data.” Nucleic Acids Research. doi:10.1093/nar/gkab552 , https://pubmed.ncbi.nlm.nih.gov/34226941/. Hanzelmann S, Castelo R, Guinney J (2013). “GSVA: gene set variation analysis for microarray and RNA-Seq data.” BMC Bioinformatics, 14(1), 7. ISSN 1471-2105, doi:10.1186/1471-2105-14-7 , http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-7.