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 1.14.0 Index]