getSequence: Retrieves sequences

In grimbough/biomaRt: Interface to BioMart databases (i.e. Ensembl)

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:

• 'cdna': for nucleotide sequences

• 'peptide': for protein sequences

• '3utr': for 3' UTR sequences

• '5utr': for 5' UTR sequences

• 'gene_exon': for exon sequences only

• 'transcript_exon_intron': gives the full unspliced transcript, that is exons + introns

• 'gene_exon_intron' gives the exons + introns of a gene;'coding' gives the coding sequence only

• 'coding_transcript_flank': gives the flanking region of the transcript including the UTRs, this must be accompanied with a given value for the upstream or downstream attribute

• 'coding_gene_flank': gives the flanking region of the gene including the UTRs, this must be accompanied with a given value for the upstream or downstream attribute

• 'transcript_flank': gives the flanking region of the transcript exculding the UTRs, this must be accompanied with a given value for the upstream or downstream attribute

• 'gene_flank': gives the flanking region of the gene excluding the UTRs, this must be accompanied with a given value for the upstream or downstream attribute

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)

}

grimbough/biomaRt documentation built on Aug. 7, 2024, 8:56 p.m.