Fetch metadata for a genomic study

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()