05 - adding or editing sample info

MitoPilot databases can be modified using several R helper functions. These functions will automatically create backups of the database in case you need to revert your changes. For more information, please see the manual pages for these functions.

Important

You must close any existing connections (e.g. the MitoPilot GUI) prior to modifying the database.

Updating sample metadata

update_sample_metadata()

Update the metadata for an existing project database. Cannot update ID, R1, or R2, but can add new metadata columns.

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” and “Taxon”
  • mapping_id: column name of the update mapping file to use as the primary key. Default = “ID”
  • mapping_taxon: column name of the update mapping file containing a Taxonomic identifier (eg, species name). Default = “Taxon”

Updating sample sequence data

update_sample_seqdata()

Update the sequence data files for samples in an existing project database. After updating, user should rerun these samples, starting with the Assemble module.

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”, “R1”, and “R2”
  • mapping_id: column name of the update mapping file to use as the primary key. Default = “ID”

Adding samples to a project

add_samples()

Add new samples to an existing project database. All samples will inherit the default processing options.

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”
  • mapping_id: column name of the update mapping file to use as the primary key. Default = “ID”
  • mapping_taxon: column name of the update mapping file containing a Taxonomic identifier (eg, species name). Default = “Taxon”