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

Description Usage Arguments Value Author(s) See Also Examples

View source: R/enrich.R

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

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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

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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.