enrichit (version 0.1.1)

ora: Over-Representation Analysis (ORA)

Description

Perform over-representation analysis using hypergeometric test (Fisher's exact test).

Usage

ora(gene, gene_sets, universe)

Value

A data.frame with columns:

GeneSet

Gene set name

SetSize

Number of genes in the gene set (intersected with universe)

DEInSet

Number of differentially expressed genes in the gene set

DESize

Total number of differentially expressed genes in universe

PValue

Raw p-value from hypergeometric test

Arguments

gene

Character vector of differentially expressed genes (or gene list of interest).

gene_sets

A named list of gene sets. Each element is a character vector of genes.

universe

Character vector of background genes (e.g., all genes in the platform).

Examples

# Example data
de_genes <- c("Gene1", "Gene2", "Gene3", "Gene4", "Gene5")
all_genes <- paste0("Gene", 1:1000)

gs1 <- paste0("Gene", 1:50)
gs2 <- paste0("Gene", 51:150)
gs3 <- paste0("Gene", 151:300)
gene_sets <- list(Pathway1 = gs1, Pathway2 = gs2, Pathway3 = gs3)

result <- ora(gene=de_genes, gene_sets=gene_sets, universe=all_genes)
head(result)