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E. coli NCBI AST Example Data, Re-interpreted with AMR Package

Source: R/data.R
ecoli_ast.Rd

A subset of E. coli phenotype data from the NCBI AST browser.

Usage

ecoli_ast

Format

ecoli_ast A data frame with 4170 rows and 10 columns representing reinterpreted data from the NCBI AST browser.

Columns include:

  • id: Sample identifier, imported from the #BioSample column in the raw input.

  • drug_agent: Antibiotic code, interpreted from Antibiotic using as.ab, used to interpret ecoff and pheno columns.

  • mic: Minimum inhibitory concentration, formatted using as.mic, used to interpret ecoff and pheno columns.

  • disk: Disk diffusion zone, formatted using as.disk, used to interpret ecoff and pheno columns.

  • pheno_clsi: S/I/R classification according to CLSI, interpreted using as.sir.

  • ecoff: WT/NWT classification, interpreted using as.sir.

  • guideline: Interpretation guidelines used to interpret ecoff and pheno columns.

  • method: Test method, one of: "Etest', "Microscan', "Phoenix', "Phoenix NMIC-203 card', "Sensititer', "Sensititre', "Vitek'.

  • pheno_provided: ??

  • spp_pheno: Species identifier, interpreted from Scientific name using as.mo, used to interpret ecoff and pheno columns.

Source

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