get_gsea_path: Gene Set Enrichment Analysis (GSEA) using Multiplex Networks

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

Gene Set Enrichment Analysis (GSEA) using Multiplex Networks

Description

This function performs gene set enrichment analysis (GSEA) based on multiplex network data.

Usage

get_gsea_path(
  seed = seed,
  network = network,
  gamma = 0.7,
  pathlist = pathlist,
  gsea.weight = 1,
  gsea.nperm = 1000
)

Arguments

seed	A seed value (optional).
network	A network object (e.g., protein-protein interaction network).
gamma	A parameter for random walk restart (default: 0.7).
pathlist	A predefined list of gene sets (pathways).
gsea.weight	Weight for GSEA (default: 1).
gsea.nperm	Number of permutations for significance testing (default: 1000).

Details

The function constructs a multiplex network, performs random walk restart, and calculates gene scores. It then transforms the scores and applies GSEA using the provided gene sets.

Value

A GSEA result object.

Examples

data(Seeds, package = "iPRISM")
data(ppi, package = "iPRISM")
data(path_list, package = "iPRISM")


result <- get_gsea_path(seed = Seeds,
                       network = ppi,
                       pathlist = path_list[1:2],
                       gsea.nperm = 100)
print(result)

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