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Example AMRFinderPlus Genotype Data from EuSCAPE project

Source: R/data.R
kp_mero_amrfp.Rd

AMRFinderPlus results file for Klebsiella pneumoniae from EuSCAPE project, one AMR determinant per row, downloaded from the EBI AMR portal using download_ebi() and imported using import_geno().

Usage

kp_mero_amrfp

Format

kp_mero_amrfp A data frame with 32,385 rows and 34 columns:

  • id: BioSample.

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

  • gene, node, marker: gene identifiers.

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

  • % Coverage of reference: % Coverage of reference.

  • % Identity to reference: % Identity to reference.

  • ...: Additional data columns from AMRFinderPlus

Source

EBI AMR Portal. See David et al. (2019) https://doi.org/10.1038/s41564-019-0492-8.