enrichMeSH: enrichMeSH

View source: R/enrichMeSH.R

enrichMeSHR Documentation

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 Nov. 12, 2022, 7:13 a.m.