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enrichNCG

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

DOSE

Disease Ontology Semantic and Enrichment analysis

v3.16.0
Artistic-2.0
Authors
Guangchuang Yu [aut, cre], Li-Gen Wang [ctb], Vladislav Petyuk [ctb], Giovanni Dall'Olio [ctb], Erqiang Hu [ctb]
Initial release

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