enrichIt: Calculate gene set enrichment scores for single-cell data

In ncborcherding/scone: Single-Cell Operation for Neat Enrichment

Description

This function allows users to input both the single-cell RNA-sequencing counts and any gene set pathways either from the stored data or from other sources. The enrichment calculation itself uses the gsva R package and the poisson distribution for RNA.

Usage

enrichIt(obj, gene.sets = NULL, groups = 1000, cores = 2)

Arguments

obj	The count matrix, Seurat, or SingleCellExperiment object.
gene.sets	Gene sets from getGeneSets to use for the enrichment analysis.
groups	The number of cells to separate the enrichment calculation.
cores	The number of cores to use for parallelization.

Value

Data frame of normalized enrichmenet scores (NES)

Author(s)

Nick Borcherding, Jared Andrews

See Also

getGeneSets to collect gene sets.

Examples

data(gsea_library)
GS <- getGeneSets(collection = gsea_library, library = "Hallmark")
GS <- GS[[1]] #Reduce list size for example
seurat_ex <- data("seurat_ex")
ES <- enrichIt(counts = seurat_ex, gene.sets = GS)

ncborcherding/scone documentation built on Sept. 5, 2020, 1:11 a.m.