biomart: Main BioMart Query Function

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/biomart.R

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

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biomart(genes, mart, dataset, attributes, filters, ...)

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, e.g. mart = "ensembl".

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".

...

additional parameters for the getBM function.

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.

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.

Author(s)

Hajk-Georg Drost

See Also

organismFilters, organismBM, listAttributes, getBM

Examples

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## Not run: 
# 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")

## End(Not run)

biomartr documentation built on July 2, 2018, 1:02 a.m.