load_mart {SWATH2stats} | R Documentation |
This function loads a biomart database
load_mart(species, ensembl.path, mart, verbose = FALSE)
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. |
Returns the mart from biomaRt.
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")
Peter Blattmann
organism.mart <- load_mart("hsapiens_gene_ensembl", "www.ensembl.org", "ENSEMBL_MART_ENSEMBL") class(organism.mart)