enrichDGNv: enrichDGN

In DOSE: Disease Ontology Semantic and Enrichment analysis

Description

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

Usage

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

Arguments

snp	a vector of SNP
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

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

DOSE documentation built on Nov. 8, 2020, 7:48 p.m.