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Retrieves sequences

Source: R/ensembl_wrappers.R
getSequence.Rd

This function retrieves sequences given the chromosome, 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 excluding 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

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)

}