pathway_enrich: Pathway Enrichment Analysis

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

Pathway Enrichment Analysis

Description

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

Usage

pathway_enrich(
  gene,
  organism = "ppu",
  keyType = "kegg",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2,
  use_internal_kegg = FALSE,
  custom_gene_sets = FALSE,
  custom_pathways = NULL
)

Arguments

gene	Character vector of gene or protein IDs to test for enrichment.
organism	KEGG organism code (e.g. "ppu").
keyType	ID type (default "kegg").
pvalueCutoff	Numeric; p‐value cutoff (default 0.05).
pAdjustMethod	Character; adjustment method (default "BH").
universe	Character vector of background IDs.
minGSSize	Integer; minimum gene set size.
maxGSSize	Integer; maximum gene set size.
qvalueCutoff	Numeric; q‐value cutoff (default 0.2).
use_internal_kegg	Logical; use internal KEGG DB if TRUE.
custom_gene_sets	Logical; use custom gene sets if TRUE.
custom_pathways	Data frame with columns "Pathway" and "Accession", or a GMT file path.

Value

An enrichResult object (or NULL if no pathways pass the thresholds).

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