Get Sequences from Ensembl

Usage

getSequence(
  chromosome,
  start,
  end,
  id,
  type,
  seqType,
  upstream,
  downstream,
  ...,
  version = NULL
)

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.
...: Ignored. Used to catch no longer necessary parameters such as mart from biomaRt functions.
version: Ensembl version to use for the query. If NULL, the latest version will be used.

Value

A data frame containing the requested sequences and their associated metadata.

Examples

# \donttest{
getSequence(
  seqType = "gene_exon_intron",
  type = "ensembl_gene_id",
  id = "ENSG00000001497"
)
#> Error in httr2::req_perform(httr2::req_body_json(httr2::req_user_agent(httr2::req_method(httr2::req_url_path(httr2::request(.construct_versioned_url(version)),     "/sequence/id"), "POST"), REMART_USER_AGENT), req)): HTTP 500 Internal Server Error.

ids <- c(
 "ENSG00000003987",
 "ENSG00000004939"
)
getSequence(
  seqType = "gene_exon_intron",
  type = "ensembl_gene_id",
  id = ids
)
#> Error in httr2::req_perform(httr2::req_body_json(httr2::req_user_agent(httr2::req_method(httr2::req_url_path(httr2::request(.construct_versioned_url(version)),     "/sequence/id"), "POST"), REMART_USER_AGENT), req)): HTTP 500 Internal Server Error.

# Retrieve sequences from a specific Ensembl release.
getSequence(
  seqType = "cdna",
  type = "ensembl_gene_id",
  id = "ENSG00000001497",
  version = 114
)
# }