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Update metadata for existing samples

Source: R/update_sample_metadata.R
update_sample_metadata.Rd

Updates metadata columns for samples already in a project's database (adding new columns if needed). Never touches R1, R2, Assembly, or any pipeline state or lock column, except that a sample whose Taxon changes has its resolved taxonomy cleared, unlocked, and queued for the Taxonomy step again. Use add_samples() to change what a sample reads or assembles from. Runs the same read_mapping()/check_mapping() checks as new_project(). Backs up the database to .old_sqlite_dbs/ first.

Usage

update_sample_metadata(
  project = ".",
  mapping_fn = NULL,
  mapping_id = "ID",
  mapping_taxon = "Taxon",
  data_path = NULL,
  assembly_path = NULL,
  check_reads = TRUE,
  check_assemblies = TRUE,
  mapping_geome = "GEOME_BCID",
  fetch_geome = TRUE,
  mapping_gbif = "GBIF_ID",
  fetch_gbif = TRUE,
  mapping_ncbi = "BioSample",
  fetch_ncbi = TRUE,
  link_sources = FALSE
)

Arguments

project

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

mapping_fn

Path to a comma-separated mapping file. Same shape as new_project()'s mapping file. Every ID must already be in the project.

mapping_id

Column in the mapping file with unique ids (default "ID").

mapping_taxon

Column in the mapping file with a taxonomic identifier (default "Taxon").

data_path

Directory holding the read files named in the mapping file (checked, not stored).

assembly_path

Directory holding the assembly files named in the mapping file (checked, not stored).

check_reads

(logical) Check that the read files named in the mapping file exist under data_path (default TRUE).

check_assemblies

(logical) Check that the assembly files named in the mapping file exist under assembly_path (default TRUE).

mapping_geome

Name of the mapping-file column holding GEOME BCIDs (optional). Stored as GEOME_BCID. See vignette("Sample-Metadata").

fetch_geome

Fetch GEOME metadata for samples with a BCID when the identifiers change (default TRUE). Set FALSE when offline and run fetch_geome() later.

mapping_gbif

Name of the mapping-file column holding GBIF occurrence IDs (optional). Stored as GBIF_ID. See vignette("Sample-Metadata").

fetch_gbif

Fetch GBIF metadata for samples with a GBIF ID when the identifiers change (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("Sample-Metadata").

fetch_ncbi

Fetch NCBI metadata for samples with a BioSample value when the identifiers change (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("Sample-Metadata").