enrichDO: DO Enrichment Analysis

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

DO Enrichment Analysis

Description

Given a vector of genes, this function will return the enrichment DO categories with FDR control.

Usage

enrichDO(
  gene,
  ont = "DO",
  organism = "hsa",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  minGSSize = 10,
  maxGSSize = 500,
  qvalueCutoff = 0.2,
  readable = FALSE
)

Arguments

gene	a vector of entrez gene id
ont	one of DO and DOLite.
organism	one of "hsa" and "mmu"
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

Value

A enrichResult instance.

Author(s)

Guangchuang Yu http://guangchuangyu.github.io

See Also

enrichResult-class

Examples

data(geneList)
	gene = names(geneList)[geneList > 1]
	yy = enrichDO(gene, pvalueCutoff=0.05)
	summary(yy)

YuLab-SMU/DOSE documentation built on April 26, 2024, 2:18 a.m.