biomart: Main BioMart Query Function

Description

This function takes a set of gene ids and the biomart specifications and performs a biomart query for the given set of gene ids.

Usage

biomart(genes, mart, dataset, attributes, filters, mute_citation = FALSE, ...)

Value

A data.table storing the initial query gene vector in the first column, the output gene vector in the second column, and all attributes in the following columns.

Arguments

genes: a character vector storing the gene ids of a organisms of interest to be queried against BioMart.
mart: a character string specifying the mart to be used. Users can obtain available marts using getMarts.
dataset: a character string specifying the dataset within the mart to be used, e.g. dataset = "hsapiens_gene_ensembl".
attributes: a character vector specifying the attributes that shall be used, e.g. attributes = c("start_position","end_position","description").
filters: a character vector specifying the filter (query key) for the BioMart query, e.g. filter = "ensembl_gene_id".
mute_citation: logical value indicating whether citation message should be muted.
...: additional parameters for the getBM function.

Author

Hajk-Georg Drost

Details

This function is the main query function of the biomartr package.

It enables to fastly access annotations of a given gene set based on the biomaRt package implemented by Steffen Durinck et al.

Examples

Run this code

if (FALSE) {
# 1) select a mart
getMarts()

# we will select mart 'plants_mart' and search for available datasets
getDatasets(mart = "plants_mart")

# we choose dataset 'athaliana_eg_gene' and run biomart()
# using mart: 'plants_mart', dataset: "athaliana_eg_gene"
# attributes: c("start_position","end_position","description")
# for an example gene set of Arabidopsis thaliana:
# c("AT1G06090", "AT1G06100", "AT1G06110", "AT1G06120",
#    "AT1G06130", "AT1G06200")

biomart(genes      = c("AT1G06090", "AT1G06100",
                       "AT1G06110", "AT1G06120",
                       "AT1G06130", "AT1G06200"),
        mart       = "plants_mart",
        dataset    = "athaliana_eg_gene",
        attributes = c("start_position","end_position","description"),
        filters    = "ensembl_gene_id")
}

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