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enrichDGNv

enrichDGN

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

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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