makeOrgDbFromBiomart: Make a OrgDb package from annotations available on a BioMart...
In altairwei/brookite: Useful bioinformation tools for R.

makeOrgDbFromBiomart

R Documentation

Make a OrgDb package from annotations available on a BioMart database

Description

Make a OrgDb package from annotations available on a BioMart database

Usage

makeOrgDbFromBiomart(
  biomart,
  tax_id,
  maintainer,
  author,
  genus = NULL,
  species = NULL,
  version = "0.0.0.9000",
  gid_type = "eg",
  outputDir = getwd()
)

Arguments

`biomart`	A Mart-class object returned by `useMart` etc.
`tax_id`	The Taxonomy ID that represents your organism. (NCBI has a nice online browser for finding the one you need)
`maintainer`	Who is the package maintainer? (must include email to be valid)
`author`	Who is the creator of this package?
`genus`	Single string indicating the genus.
`species`	Single string indicating the species.
`version`	What is the version number for this package? format: \'x.y.z\'
`gid_type`	the type of central identifier.
`outputDir`	A path where the package source should be assembled.

Examples

mart <- biomaRt::useMart(
  biomart = "plants_mart",
  version = "Ensembl Plants Genes 52",
  dataset = "taestivum_eg_gene",
  host = "https://plants.ensembl.org"
)

makeOrgDbFromBiomart(
  biomart = mart,
  version = "0.0.0.9000",
  maintainer = "Altair Wei <altair_wei@outlook.com>",
  author = "Altair Wei <altair_wei@outlook.com>",
  outputDir = ".",
  tax_id = "4565",
  genus = "Triticum",
  species = "aestivum",
  gid_type = "iwgsc"
)

altairwei/brookite documentation built on Nov. 1, 2022, 7:03 p.m.