enrichMeSH: enrichMeSH

In GuangchuangYu/meshes: MeSH Enrichment and Semantic analyses

enrichMeSH

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,
  meshdbVersion = NULL
)

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
meshdbVersion	version of MeSH.db. If NULL(the default), use the latest version.

Value

An enrichResult instance.

Author(s)

Guangchuang Yu

See Also

class?enrichResult

Examples

## Not run: 
library(meshes)
library(AnnotationHub)
ah <- AnnotationHub()
qr_hsa <- query(ah, c("MeSHDb", "Homo sapiens"))
filepath_hsa <- qr_hsa[[1]]
db <- MeSHDbi::MeSHDb(filepath_hsa)
data(geneList, package="DOSE")
de <- names(geneList)[1:100]
x <- enrichMeSH(de, MeSHDb = db, database='gendoo', category = 'C')

## End(Not run)

GuangchuangYu/meshes documentation built on Feb. 9, 2024, 3:05 a.m.