iPRISM (version 0.1.1)

get_gsea_path: 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
)

Value

A GSEA result object.

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.

Examples

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

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