load_mart: Establish connection to biomaRt database

Description Usage Arguments Value Author(s) Examples

View source: R/convert_protein_ids.R

Description

This function establishes a connection to a biomart database.

Usage

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load_mart(species, ensembl.path = "www.ensembl.org", 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

Ensembl host to connect to. Default: www.ensembl.org

mart

The type of mart (e.g. "ENSEMBL_MART_ENSEMBL", etc.)

verbose

print a summary of the ensembl connection.

Value

Connection for performing biomart queries.

Author(s)

Peter Blattmann

Examples

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{
 data_table <- data.frame(Protein = c("Q01581", "P49327", "2/P63261/P60709"),
                          Abundance = c(100, 3390, 43423))
 mart <- convert_protein_ids(data_table)
 }

peterblattmann/SWATH2stats documentation built on April 20, 2021, 12:02 p.m.