Skip to contents

S. aureus Example of Imported NCBI Phenotype Data

Source: R/data.R
staph_ast_ncbi.Rd

Phenotypes sourced from NCBI Biosamples using the download_ncbi_ast function and imported to AMRgen phenotype table format.

Usage

staph_ast_ncbi

Format

staph_ast_ncbi A data frame with 143 rows and 19 columns representing all Staphylococcus aureus phenotyping results for amikacin and doxycycline downloaded from NCBI using download_ncbi_ast, imported into AMRgen format using import_ast.

Columns include:

  • id: Sample identifier.

  • drug_agent: Antibiotic identifier, as class 'ab'.

  • mic: MIC data, as class 'mic'.

  • disk: Disk diffusion zone diameter data, as class 'disk'.

  • pheno_provided, pheno_eucast: S/I/R phenotypes as downloaded from NCBI, and as re-interpreted from mic/disk measures against EUCAST 2024 breakpoints.

  • ...: Additional data columns from NCBI.

Source

https://www.ncbi.nlm.nih.gov/pathogens/ast