fetchMetadata: Fetch metadata for a genomic study

In hugheylab/seeker: Simplified Fetching and Processing of Microarray and RNA-Seq Data

Fetch metadata for a genomic study

Description

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()

hugheylab/seeker documentation built on Aug. 28, 2024, 8:20 a.m.