biomartr (version 0.0.1)

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, ...)

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.

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

Examples

# the initial biomaRt workflow would work as follows:

# 1) select a mart and data set
mart <- useDataset("athaliana_eg_gene", mart = useMart("plants_mart_25"))

# 2) run a biomart query using the getBM() function
# and specify the attributes and filter arguments
geneSet <- c("AT1G06090", "AT1G06100",
             "AT1G06110", "AT1G06120",
             "AT1G06130", "AT1G06200")

resultTable <- getBM(attributes = c("start_position","end_position","description"),
                     filters = "tair_locus", values = geneSet, mart = mart)

# for faster query access and easier query logic the
# biomart() function combines this workflow

# using mart: 'plants_mart_25', 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_25",
        dataset    = "athaliana_eg_gene",
        attributes = c("start_position","end_position","description"),
        filters    = "tair_locus")