get_topGO_data: Create topGO data and enrichment analysis

In HCGB-IGTP/HCGB.IGTP.DAnalysis: Useful in-house functions for multiple analysis

Create topGO data and enrichment analysis

Description

Creates Gene Ontology data using topGO package and enrichment analysis

Usage

get_topGO_data(
  list_genes,
  list_all_genes,
  gene2GO,
  ont_given = "B",
  nodeSize_given = 5,
  cutoff_given = 0.05,
  statistic_given = "fisher"
)

Arguments

list_genes	List of DE gene (EntrezID).
list_all_genes	List of all available genes (EntrezID).
ont_given	Ontology to analyse: Biological process (B); Mollecular function (M) or Celullar component (C)
nodeSize_given	Size of the node used to prune the GO hierarchy from the terms which have less than X annotated genes
cutoff_given	Pvalue cutoff given
gene2go	ViSEAGO annotation object for the package annotation of interest.

HCGB-IGTP/HCGB.IGTP.DAnalysis documentation built on April 13, 2025, 12:03 a.m.