gseMeSH: gseMeSH

View source: R/gseMeSH.R

gseMeSHR Documentation

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