Main BioMart Query Function — biomart • biomartr
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.

# Main BioMart Query Function

Source: `R/biomart.R`
`biomart.Rd`

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

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

## 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.

## 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.

## 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.

## See also

`organismFilters`, `organismBM`, `listAttributes`, `getBM`

## Author

Hajk-Georg Drost

## Examples

    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")
    }