gseMeSH {meshes} | R 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)

[Package meshes version 1.20.0 Index]