getSequence {biomaRt}R Documentation

Retrieves sequences

Description

This function retrieves sequences given the chomosome, start and end position or a list of identifiers. Using getSequence in web service mode (default) generates 5' to 3' sequences of the requested type on the correct strand.

Usage

getSequence(chromosome, start, end, id, type, seqType, 
                   upstream, downstream, mart, useCache = TRUE, verbose = FALSE)

Arguments

chromosome

Chromosome name

start

start position of sequence on chromosome

end

end position of sequence on chromosome

id

An identifier or vector of identifiers.

type

The type of identifier used. Supported types are hugo, ensembl, embl, entrezgene, refseq, ensemblTrans and unigene. Alternatively one can also use a filter to specify the type. Possible filters are given by the listFilters() function.

seqType

Type of sequence that you want to retrieve. Allowed seqTypes are given in the details section.

upstream

To add the upstream sequence of a specified number of basepairs to the output.

downstream

To add the downstream sequence of a specified number of basepairs to the output.

mart

object of class Mart created using the useEnsembl function

useCache

If useCache = TRUE then biomaRt will try to store succesful query results on disk, and will load these if a query is run again, rather than contacting the Ensembl server.

verbose

If verbose = TRUE then the XML query that was send to the webservice will be displayed.

Details

The type of sequence returned can be specified by the seqType argument which takes the following values:

Author(s)

Steffen Durinck, Mike Smith

Examples

if(interactive()){
mart <- useEnsembl("ensembl", dataset="hsapiens_gene_ensembl")

seq = getSequence(id = "BRCA1", 
                  type = "hgnc_symbol", 
                  seqType = "peptide", 
                  mart = mart)
show(seq)

seq = getSequence(id="1939_at", 
                  type="affy_hg_u95av2", 
                  seqType="gene_flank",
                  upstream = 20, 
                  mart = mart)
show(seq)

}

[Package biomaRt version 2.48.1 Index]