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E. coli genotype data from Mills et al 2022

Source: R/data.R
geno_eco_2075.Rd

Genotyping data for isolates published in Mills et al, Genome Medicine (2022) 14:147, generated using AMRfinderplus v3.12.8 and downloaded from the AllTheBacteria project, and imported to AMRgen genotype table format. Corresponding MIC data is available in pheno_eco_2075.

Usage

geno_eco_2075

Format

geno_eco_2075 A data frame with 56064 rows and 24 columns representing AMRfinderplus genotyping results for 2075 E. coli isolates.

Columns include:

  • id: Sample identifier.

  • drug_agent, drug_class: Antibiotic agent and class, determined by parsing AMRfinderplus subclass field in the downloaded file.

  • gene, node, marker: gene symbol, parsed from amr_element_symbol field in the downloaded file.

  • mutation: mutation within gene, parsed into HGVS nomenclature format from amr_element_symbol field in the downloaded file.

  • marker.label: label for genotype marker, combining gene and mutation information (deletion variants represented as "gene:-").

  • ...: Additional data columns from AMRfinderplus

Source

https://github.com/AllTheBacteria/AllTheBacteria