enrichNCG: enrichNCG

In YuLab-SMU/DOSE: Disease Ontology Semantic and Enrichment analysis

enrichNCG

Description

Enrichment analysis based on the Network of Cancer Genes database (http://ncg.kcl.ac.uk/)

Usage

enrichNCG(
  gene,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2,
  readable = FALSE
)

Arguments

gene	a vector of entrez gene id
pvalueCutoff	pvalue cutoff
pAdjustMethod	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
universe	background genes
minGSSize	minimal size of genes annotated by NCG category for testing
maxGSSize	maximal size of each geneSet for analyzing
qvalueCutoff	qvalue cutoff
readable	whether mapping gene ID to gene Name

Details

given a vector of genes, this function will return the enrichment NCG categories with FDR control

Value

A enrichResult instance

Author(s)

Guangchuang Yu

YuLab-SMU/DOSE documentation built on Nov. 3, 2024, 9:37 p.m.