getStrains: Downloads BacDive strains from a list of supplied ID's

In scottdaniel/bacphene: Imports Bacterial Phenotype Data Into R

Downloads BacDive strains from a list of supplied ID's

Description

Downloads BacDive strains from a list of supplied ID's

Usage

getStrains(
  strain_list = "data-raw/full_list_of_bacteria_from_bacdive_20211027.csv",
  typestrain_only = T,
  bacdive_keycloak = getBacDiveAccess(),
  rda = "data-raw/strain_large_list.rda"
)

Arguments

strain_list	A csv file containing at least two columns: "ID" - The BacDive ID and "is_type_strain_header". Can be gotten using BacDive's advanced search.
typestrain_only	Whether to filter down to typestrains only.
bacdive_keycloak	A 'dsmz_keycloak' object that allows access to the BacDive API. Created using getBacDiveAccess or open_bacdive.
save_rda	If this is being run for the first time, the list of strains will be saved to the specificed RData file. Otherwise, the function will load strains from the specified data file.

Value

A list object of strain information. If running for the first time, saves an RData file of the list.

Examples

## Not run: 
large_list <- getStrains(strain_list = "my_csv_file.csv", typestrain_only = F)

## End(Not run)

scottdaniel/bacphene documentation built on March 25, 2023, 12:51 p.m.