Fetch metadata for a genomic study — fetchMetadata • seeker

This function can use the API of the European Nucleotide Archive (recommended) or the Sequence Read Archive.

Usage

fetchMetadata(
  bioproject,
  host = c("ena", "sra"),
  fields = c("study_accession", "sample_accession", "secondary_sample_accession",
    "sample_alias", "sample_title", "experiment_accession", "run_accession", "fastq_md5",
    "fastq_ftp", "fastq_aspera"),
  file = NULL
)

Arguments

bioproject: String indicating bioproject accession.
host: String indicating from where to fetch the metadata.
fields: Character vector indicating which fields to fetch, if host is "ena".
file: String indicating output file path, if not NULL.

Value

A data.table.

See also

seeker(), fetch()