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Run Gene Set Enrichment Analysis on a Reduction

Source: R/Seurat_wrapper.R
RunGSEA.Rd

Run GSEA to identify gene sets that are enriched within NMF factors.

Usage

RunGSEA(
  object,
  reduction = "nmf",
  species = "Homo sapiens",
  category = "C5",
  min.size = 10,
  max.size = 500,
  dims = NULL,
  verbose = TRUE,
  padj.sig = 0.01
)

Arguments

object

a Seurat object

reduction

dimensional reduction to use

species

species for which to load gene sets

category

msigdbr gene set category (i.e. "H", "C5", etc.)

min.size

minimum number of terms in a gene set

max.size

maximum number of terms in a gene set

dims

factors in the reduction to use, default NULL for all factors

verbose

print progress to console

padj.sig

significance cutoff for BH-adjusted p-values (default 0.01)

Value

a Seurat object, with GSEA information in the misc slot. BH-adj p-values are on a -log10 scale.