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S. aureus Example of Imported EBI Genotype Data

Source: R/data.R
staph_geno_ebi.Rd

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

Usage

staph_geno_ebi

Format

staph_geno_ebi A data frame with 198344 rows and 34 columns representing all Staphylococcus genotyping results downloaded from EBI using download_ebi, and imported into AMRgen format using import_amrfp.

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 EBI.

Source

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