gseMeSH {meshes}R Documentation

gseMeSH

Description

Gene Set Enrichment Analysis of MeSH

Usage

gseMeSH(geneList, MeSHDb, database = "gendoo", category = "C",
  exponent = 1, nPerm = 1000, minGSSize = 10, maxGSSize = 500,
  pvalueCutoff = 0.05, pAdjustMethod = "BH", verbose = TRUE,
  seed = FALSE, by = "fgsea")

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

nPerm

permutation numbers

minGSSize

minimal size of each geneSet for analyzing

maxGSSize

maximal size of genes annotated for testing

pvalueCutoff

pvalue Cutoff

pAdjustMethod

pvalue adjustment method

verbose

print message or not

seed

logical

by

one of 'fgsea' or 'DOSE'

Value

gseaResult object

Author(s)

Yu Guangchuang

Examples

## Not run: 
data(geneList, package="DOSE")
y <- gseMeSH(geneList, MeSHDb = "MeSH.Hsa.eg.db", database = 'gene2pubmed', category = "G")

## End(Not run)

[Package meshes version 1.6.1 Index]