gimme_mart: Handy function to create a biomaRt R object based on the...

In Ni-Ar/niar: Nice Interactive Analysis with R

Handy function to create a biomaRt R object based on the ENSEMBL database to be used when querying biomart

Description

A function to get a biomaRt object during an R analysis that can later on be used for retrieving gene IDs, coordinates and more.

Usage

gimme_mart(
  species = "hsapiens",
  version = "latest",
  verbose = TRUE,
  out_dir = FALSE,
  use_mirror = FALSE,
  which_mirror
)

Arguments

species	a character specifying the species to work with. Currently the supported species are: hsapiens - Human (Homo Sapiens) Default mmulatta - Rhesus Macaque (Macaca mulatta) mmusculus - Mouse (Mus Musculus) rnorvegicus - Rat (Rattus Norvegicus) btaurus - Cattle, aka Cows & Bulls (Bos Taurus) mdomestica - Gray short-tailed Opossum (Monodelphis domestica) ggallus - Chicken (Gallus Gallus)
version	Which database version of biomart do you want? Use: latest - for the latest version of the database. penultimate - for the one before the latest version of the database. number - a specific version of the biomart database. If the version you query is not available an error is returned.
verbose	Logical. Print the version and genome assembly for the species queried. Default TRUE.
out_dir	Either FALSE (default) or a character specifying a path where to save the biomaRt object. If directory does not exist it will be created.
use_mirror	Logical. Do you want to use a mirror for creating the biomart object? Default FALSE. If TRUE the parameter version will be converted to TRUE.
which_mirror	Specify which biomart mirror to use. Chose from: www - UK (Sanger Institute). in Cambridge, default uswest - US West (Amazon AWS) on West Coast of US of America useast - US East (Amazon AWS) on East Coast of US of America asia - Asia (Amazon AWS) in Singapore

Value

A biomaRt ensembl object

Note

The latest ensembl release version of the mouse genome GRCm38 (aka mm10) is 102.

Examples

# Human ENSEMBL biomaRt object
human_ensembl <- gimme_mart()

Ni-Ar/niar documentation built on Feb. 3, 2025, 9:25 a.m.