fromEnsembl: build annotation from ensembl

In guokai8/bioAnno: Build Annotation From Online Database

build annotation from ensembl

Description

build annotation from ensembl

build annotation from ensembl

Usage

fromEnsembl(
  species = "Caenorhabditis elegans",
  host = NULL,
  anntype = NULL,
  buildall = TRUE,
  author = NULL,
  maintainer = NULL,
  tax_id = NULL,
  genus = NULL,
  version = NULL,
  plant = FALSE,
  install = TRUE,
  pkgname = NULL,
  outputDir = NULL,
  rebuild = FALSE
)

Arguments

species	the sepcies you want to search, you can use listSpecies to get the species name
host	the ensemble API host,for plant you can use plants.ensembl.org and for human and other species you can use uswest.ensembl.org
anntype	the type of function annotation(GO,KEGG,PFAM,InterPro) you want get from ensemble
buildall	include all prossbile annoation type listed in Ensembl
author	author for the annotation package
maintainer	maintainer for the annotation package
tax_id	taxonomy id for the species
genus	genus name for the annotation package
version	version number for the annotation package
plant	plant or animal species (TRUE/FALSE)
install	install the package or not(default: TRUE)
pkgname	package name you want to choose
outputDir	temporary output path
rebuild	rebuild the package or not(default: FALSE)

Value

annotation package

Author(s)

Kai Guo

Examples

fromEnsembl(species = "Caenorhabditis elegans", anntype="GO")

guokai8/bioAnno documentation built on May 8, 2023, 12:42 p.m.