gseMeSH: gseMeSH

In GuangchuangYu/meshes: MeSH Enrichment and Semantic analyses

gseMeSH

Description

Gene Set Enrichment Analysis of MeSH

Usage

gseMeSH(
  geneList,
  MeSHDb,
  database = "gendoo",
  category = "C",
  exponent = 1,
  minGSSize = 10,
  maxGSSize = 500,
  eps = 1e-10,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  verbose = TRUE,
  seed = FALSE,
  by = "fgsea",
  meshdbVersion = NULL,
  ...
)

Arguments

geneList	order ranked geneList
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"
exponent	weight of each step
minGSSize	minimal size of each geneSet for analyzing
maxGSSize	maximal size of genes annotated for testing
eps	This parameter sets the boundary for calculating the p value.
pvalueCutoff	pvalue Cutoff
pAdjustMethod	pvalue adjustment method
verbose	print message or not
seed	logical
by	one of 'fgsea' or 'DOSE'
meshdbVersion	version of MeSH.db. If NULL(the default), use the latest version.
...	other parameter

Value

gseaResult object

Author(s)

Yu Guangchuang

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")
y <- gseMeSH(geneList, MeSHDb = db, database = 'gene2pubmed', category = "G")

## End(Not run)

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