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Add samples to an existing project

Source: R/add_samples.R
add_samples.Rd

Appends new samples to a project's database, seeding every per-sample table (samples, preprocess, assemble, annotate) the way new_db() does for a new sample. Runs the same read_mapping()/check_mapping() checks as new_project().

Usage

add_samples(
  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 for the new samples only. Same shape as new_project()'s mapping file: an ID column (none already in the project), a Taxon column, and R1/R2 columns naming paired read files relative to data_path (or an Assembly column). Column names are matched ignoring case. Extra metadata columns are added to the samples table if not already present.

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 where the new samples' raw read data is located. Defaults to the project's read folder (rawDir in its .config), and must be that folder.

assembly_path

Directory holding the new samples' assembly files named in the mapping file's optional Assembly column. Defaults to the project's assembly folder (asmbDir in its .config), and must be that folder.

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 samples are added (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 samples are added (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 samples are added (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").