geneSetEval: Gene Set Enrichment Analysis for Clusters from scRNA-seq...

In cindyfang70/clustREval: Evaluates Clustering

Description

A function that uses MSigDB Hallmark Pathways to compute gene set enrichment analysis for each clustering output given in clusters.

Usage

geneSetEval(sce, clusters, gmtPathway)

Arguments

sce	A SingleCellExperiment object with raw counts in the counts slot.
clusters	Factor representing clustering results from a pipeline for the SingleCellExperiment.
gmtPathway	File path pointing to a .gmt file for gene set analysis.

Value

Tibble containing gene set enrichment results for all clusters.

Examples

# Example:
## Not run: 
data(embryo)
data(embryoClusts)
# Compute pathways for the first clustering output by accessing raw data provided for pathways file
GMTPath <- system.file("extdata", "h.all.v7.4.symbols.gmt", package = "clustREval")
geneSetRes <- geneSetEval(embryo, embryoClusts[[1]], GMTPath)
geneSetRes

## End(Not run)

cindyfang70/clustREval documentation built on Dec. 19, 2021, 4:59 p.m.