run_fgsea_from_de: Run GSEA Using fgsea

In eisascience/scCustFx: single-cell custom fxs Package

Run GSEA Using fgsea

Description

Performs preranked GSEA and returns results for plotting.

Usage

run_fgsea_from_de(
  de_df,
  species = "Homo sapiens",
  category = "H",
  subcategory = NULL,
  method = "multilevel",
  top_n = 10
)

Arguments

de_df	A data frame with 'gene' and 'log2FoldChange' columns.
species	Character. Species name for msigdbr (default: "Homo sapiens").
category	Character. MSigDB category (default: "H").
subcategory	Character. Optional subcategory (e.g., "CP:KEGG").
method	Character. "multilevel" (default) or "simple".
top_n	Integer. Number of top pathways to return.

Value

A data frame of GSEA results sorted by p-value.

eisascience/scCustFx documentation built on June 2, 2025, 3:59 a.m.