scPipeline (version 0.2.0.0)

ReactomeData: Reactome Data Analysis for Seurat Object

Description

This function performs pathway analysis using ReactomeGSA on a Seurat object with cluster information.

Usage

ReactomeData(lowdim_seurat_object)

Value

A list containing: - GSVA result (gsva_result) - Pathway expression data (pathway_expression) - Max difference between pathway expression values (max_difference)

Arguments

lowdim_seurat_object

Seurat object that has clusters information

Examples

# \donttest{
library(Seurat)
# Read 10X counts data from matrix.mtx, barcodes.tsv and genes.tsv
counts <- Read10X(data.dir = "../inst/extdata", gene.column = 1)

# Create Seurat object without batch correction
seurat_obj <- SeuratPreprocess(counts)
seurat_obj <- SeuratLowDim(seurat_obj)
# Reactome Analysis
seurat_reactome <- ReactomeData(seurat_obj)
# }