gseafun {iPRISM} | R Documentation |
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)
[Package iPRISM version 0.1.1 Index]