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S. aureus Example of Imported EBI Phenotype Data

Source: R/data.R
staph_ast_ebi.Rd

Phenotypes sourced from EBI AMR Portal using the download_ebi function and imported to AMRgen phenotype table format.

Usage

staph_ast_ebi

Format

staph_ast_ebi A data frame with 218 rows and 46 columns representing all Staphylococcus phenotyping results for amikacin and doxycycline downloaded from EBI using download_ebi, and 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, pheno_clsi, ecoff: S/I/R phenotypes as downloaded from EBI, and as re-interpreted from mic/disk measures against EUCAST 2024 breakpoints.

  • ...: Additional data columns from EBI.

Source

https://www.ebi.ac.uk/amr