gseafun: Gene Set Enrichment Analysis (GSEA) Function

In iPRISM: Intelligent Predicting Response to Cancer Immunotherapy Through Systematic Modeling

Gene Set Enrichment Analysis (GSEA) Function

Description

This function performs gene set enrichment analysis using a gene list and a set of pathways.

Usage

gseafun(genelist, pathlist, nperm = 1000, weighted = 1)

Arguments

genelist	A named vector of gene expression values.
pathlist	A list of gene sets (pathways) to test for enrichment.
nperm	Number of permutations for calculating p-values (default is 1000).
weighted	Logical indicating whether to use weighted enrichment scores (default is TRUE).

Value

A data frame with enrichment scores (ES), p-values, and adjusted p-values.

Examples

data(path_list, package = "iPRISM")
data(genelist_imm, package = "iPRISM")

res_gsea_imm <- gseafun(genelist = genelist_imm,
                        pathlist = path_list[1:2],
                        weighted = 1,
                        nperm = 1000)
print(res_gsea_imm)

iPRISM documentation built on Sept. 11, 2024, 7:14 p.m.