getMesh {geneset}

Get MeSH geneset and geneset_name MeSH is the annotation used for MEDLINE/PubMed articles and is manually curated by NLM (U.S. National Library of Medicine). Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Description

Get MeSH geneset and geneset_name MeSH is the annotation used for MEDLINE/PubMed articles and is manually curated by NLM (U.S. National Library of Medicine). Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Usage

getMesh(
  org = "human",
  method = c("gendoo", "gene2pubmed", "RBBH"),
  category = c("A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "Z"),
  download.method = NULL,
  data_dir = NULL
)

Arguments

org

Organism mesh_name from 'mesh_org'.

method

Method of mapping MeSH ID to gene ID. Choose one from "gendoo", "gene2pubmed" or "RBBH" (mainly for some minor species). See also 'mesh_metadata'.

category

MeSH descriptor categories from 'mesh_metadata' (refer to: https://wikipedia.org/wiki/List_of_MeSH_codes).

download.method

"auto" (as default if NULL), "wininet" (for windows)

data_dir

data saving location, default is the package data directory

Value

A list including geneset and geneset name.

Examples

x = getMesh(org = "human", method = "gendoo", category = "A", data_dir = tempdir())