enrichMeSH: enrichMeSH

In meshes: MeSH Enrichment and Semantic analyses

Description

MeSH term enrichment analysis

Usage

enrichMeSH(
  gene,
  MeSHDb,
  database = "gendoo",
  category = "C",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  universe,
  qvalueCutoff = 0.2,
  minGSSize = 10,
  maxGSSize = 500
)

Arguments

gene	a vector of entrez gene id
MeSHDb	MeSHDb
database	one of 'gendoo', 'gene2pubmed' or 'RBBH'
category	one of "A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L","M", "N", "V", "Z"
pvalueCutoff	Cutoff value of pvalue.
pAdjustMethod	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
universe	background genes
qvalueCutoff	qvalue cutoff
minGSSize	minimal size of genes annotated by Ontology term for testing.
maxGSSize	maximal size of genes annotated for testing

Value

An enrichResult instance.

Author(s)

Guangchuang Yu

See Also

class?enrichResult

Examples

## Not run: 
data(geneList, package="DOSE")
de <- names(geneList)[1:100]
x <- enrichMeSH(de, MeSHDb = "MeSH.Hsa.eg.db", database='gendoo', category = 'C')

## End(Not run)

meshes documentation built on Nov. 8, 2020, 4:58 p.m.