enrichDGN: Enrichment analysis based on the DisGeNET...
In YuLab-SMU/DOSE: Disease Ontology Semantic and Enrichment analysis

enrichDGN

R Documentation

Enrichment analysis based on the DisGeNET (http://www.disgenet.org/)

Description

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

Usage

enrichDGN(
  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

Value

A enrichResult instance

Author(s)

Guangchuang Yu

References

Janet et al. (2015) DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database bav028 http://database.oxfordjournals.org/content/2015/bav028.long

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