getOrg {MAGeCKFlute}R Documentation

Determine the gene annotation package.

Description

Determine the gene annotation package. for specific organism

Usage

getOrg(organism, update = FALSE)

Arguments

organism

Character, KEGG species code, or the common species name, used to determine the gene annotation package. For all potential values check: data(bods); bods. Default org="hsa", and can also be "human" (case insensitive).

update

Boolean, indicating whether download recent annotation from NCBI.

Value

A list containing three elements:

organism

species

pkgannotation package name Symbol_Entreza data frame, mapping between gene symbol and entrez id

Author(s)

Wubing Zhang

Examples

ann = getOrg("human")
print(ann$pkg)


[Package MAGeCKFlute version 1.0.1 Index]