refdb_set_fields: Associate columns to fields
In refdb: A DNA Reference Library Manager

refdb_set_fields

R Documentation

Associate columns to fields

Description

Associate columns to fields so they are recognized and appropriately treated by refdb functions.

Usage

refdb_set_fields(
  x,
  source = NA,
  id = NA,
  organism = NA,
  taxonomy = NA,
  sequence = NA,
  marker = NA,
  latitude = NA,
  longitude = NA,
  reference = NA,
  config_yaml = NULL
)

Arguments

`x`	a reference database (tibble).
`source`	name of the column which contains the data source.
`id`	name of the column which contains the record IDs.
`organism`	name of the column which contains the names of the organisms.
`taxonomy`	a vector of column names.
`sequence`	name of the column which contains the sequences.
`marker`	name of the column which contains marker names.
`latitude`	name of the column which contains latitudes (WGS 84)
`longitude`	name of the column which contains longitudes (WGS 84).
`reference`	a vector of column names.
`config_yaml`	a file path to a YAML file

Details

Taxonomy reordering. NA to ignore, NULL to delete. Fields set using config_yaml always overwrite those set by arguments

Value

The function returns x with updated attributes.

Examples

lib <- read.csv(system.file("extdata", "ephem.csv", package = "refdb"))
lib <- refdb_set_fields(lib,
                        taxonomy = c(family = "family_name",
                            genus = "genus_name",
                            species = "species_name"),
                        sequence = "DNA_seq",
                        marker = "marker")

refdb documentation built on Sept. 22, 2022, 5:07 p.m.