Get Sequences from Ensembl

Usage

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

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.

Value

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

Examples

remart::getSequence(
  seqType = "gene_exon_intron",
  type = "ensembl_gene_id",
  id = "ENSG00000001497"
)

ids <- c(
 "ENSG00000003987",
 "ENSG00000004939"
)
remart::getSequence(
  seqType = "gene_exon_intron",
  type = "ensembl_gene_id",
  id = ids
)