Perform Gene Set Enrichment Analysis (GSEA) on Seurat object

Source: R/RunGSEA.R

Perform Gene Set Enrichment Analysis (GSEA) on Seurat object. GSEA is implemented using clusterProfiler package.

RunGSEA(
  SeuratObj,
  by = "GO",
  TERM2GENE = NULL,
  minpct = 0,
  pvalueCutoff = 1,
  category = NULL,
  subcategory = NULL
)

Arguments

SeuratObj

Seurat object
by

GO KEGG Reactome MSigDb WikiPathways DO NCG DGN. May be a character vector. Will be ignored if parameter "TERM2GENE" is not NULL.
TERM2GENE

Customized terms. Annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene. NULL by default. If not NULL, parameter "by" will be ignored.
minpct

minimum expression percent in each cluster, parameter used to filter Differential expression genes to run GSEA. 0 as default.
pvalueCutoff

threshold of p-value in GSEA result
category

MSigDB collection abbreviation, such as H, C1, C2, C3, C4, C5, C6, C7. If NULL, all gene sets.
subcategory

MSigDB sub-collection abbreviation, such as CGP or BP.

Value

Seurat object

Examples

if (FALSE) {
SeuratObj <- RunGSEA(SeuratObj, by = 'GO')
}