enrich_pathways: Enrichment analysis of pathways

In NicWir/VisomX: User-Friendly and Comprehensive Analysis and Visualization of Omics Data

Enrichment analysis of pathways

Description

Performs over‐representation testing via DOSE/clusterProfiler against KEGG or custom gene sets.

Usage

enrich_pathways(
  object,
  contrasts,
  alpha_pathways = 0.1,
  pathway_kegg = TRUE,
  kegg_organism,
  custom_pathways = NULL
)

Arguments

object	A DESeqDataSet or SummarizedExperiment object.
contrasts	A character vector of contrasts to test. Example: c("A_vs_B", "C_vs_D").
alpha_pathways	Numeric; p‐value cutoff (default 0.1).
pathway_kegg	Logical; use KEGG pathways if TRUE.
kegg_organism	KEGG organism code (e.g. "ppu").
custom_pathways	Data frame with columns "Pathway" and "Accession", or a GMT file path.

Value

A list of pathway enrichment results for each contrast.

NicWir/VisomX documentation built on July 17, 2025, 12:08 a.m.