getKEGG: Get KEGG geneset and geneset_name Geneset is a data.frame of...

In geneset: Get Gene Sets for Gene Enrichment Analysis

Get KEGG geneset and geneset_name 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 KEGG geneset and geneset_name 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

getKEGG(
  org = "hsa",
  category = c("pathway", "module", "enzyme", "disease", "drug", "network"),
  download.method = NULL,
  data_dir = NULL
)

Arguments

org	Organism name from 'kegg_org'.
category	Choose one category from "pathway","module", "enzyme", 'disease' (human only),'drug' (human only) or 'network' (human only)
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 = getKEGG(org = "hsa",category = "pathway", data_dir = tempdir())

geneset documentation built on Nov. 20, 2022, 9:07 a.m.