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Add samples to project database

Source: R/add_samples.R
add_samples.Rd

Add new samples to an existing project database. All samples will inherit the default processing options. Creates a backup of the existing database prior to updating.

Usage

add_samples(
  path = ".",
  update_mapping_fn = NULL,
  mapping_id = "ID",
  mapping_taxon = "Taxon",
  mapping_geome = "GEOME_BCID",
  fetch_geome = TRUE,
  mapping_gbif = "GBIF_ID",
  fetch_gbif = TRUE,
  mapping_ncbi = "BioSample",
  fetch_ncbi = TRUE,
  link_sources = FALSE
)

Arguments

path

Path to the project directory (default = current working directory)

update_mapping_fn

Path to the update mapping CSV file. Must contain columns "ID", "Taxon, "R1", and "R2". May include additional columns with other sample metadata, and an optional Reference column naming a per-sample MapToRef reference (file path, URL, or NCBI accession). A FASTA reference also needs a Reference_topology column (circular or linear). Both values are stored on the sample and used when its parameter set assembles with MapToRef. Reference is a reserved column name: it is never stored as sample metadata, so rename the column if you use it for something else.

mapping_id

Column name of the update mapping file to use as the primary key

mapping_taxon

Column name of the update mapping file containing a Taxonomic identifier (eg, species name)

mapping_geome

Name of the mapping-file column holding GEOME BCIDs

fetch_geome

Fetch GEOME metadata for samples with a BCID during setup (default TRUE). Set FALSE when offline and run [fetch_geome()] later.

mapping_gbif

Name of the mapping-file column holding GBIF occurrence IDs

fetch_gbif

Fetch GBIF metadata for samples with a GBIF ID (default TRUE). Set FALSE when offline and run [fetch_gbif()] later.

mapping_ncbi

Name of the mapping-file column holding NCBI BioSample or SRA accessions (optional). Must not be the sample ID column. Stored as `BioSample`. See `vignette("Specimen-Metadata")`.

fetch_ncbi

Fetch NCBI metadata for samples with a BioSample value (default TRUE). Set FALSE when offline and run [fetch_ncbi()] later.

Follow links between GEOME, GBIF, and NCBI records for these samples (default FALSE). Linking also runs when the project setting is on; this argument does not change the setting. See `vignette("Specimen-Metadata")`.