load_mart {SWATH2stats}R Documentation

load_mart: Load a biomart database

Description

This function loads a biomart database

Usage

load_mart(species, ensembl.path, mart, verbose = FALSE)

Arguments

species

The species of the protein identifiers in the term used by biomaRt (e.g. "hsapiens_gene_ensembl", "mmusculus_gene_ensembl", "drerio_gene_ensembl", etc.)

ensembl.path

Path of the biomaRt database.

mart

The species of the protein identifiers in the term used by biomaRt (e.g. "hsapiens_gene_ensembl", "mmusculus_gene_ensembl", "drerio_gene_ensembl", etc.)

verbose

Option to write a file containing the version of the database used.

Value

Returns the mart from biomaRt.

Note

Protein identifiers from shared peptides should be separated by a forward slash. The host of archived ensembl databases can be introduced as well (e.g. "dec2017.archive.ensembl.org")

Author(s)

Peter Blattmann

Examples

organism.mart <- load_mart("hsapiens_gene_ensembl", "www.ensembl.org", "ENSEMBL_MART_ENSEMBL")
class(organism.mart)

[Package SWATH2stats version 1.16.0 Index]