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Import and Process AMRFinderPlus Results

Source: R/import_geno.R
import_amrfp.Rd

This function imports and processes AMRFinderPlus results, extracting antimicrobial resistance (AMR) elements and mapping them to standardised antibiotic names and drug classes. The function also converts gene symbols to a harmonised format and ensures compatibility with the AMR package.

Usage

import_amrfp(
  input_table,
  sample_col = "Name",
  element_symbol_col = NULL,
  element_type_col = NULL,
  element_subtype_col = "Element subtype",
  method_col = "Method",
  node_col = "Hierarchy node",
  subclass_col = "Subclass",
  class_col = "Class",
  amrfp_drugs = amrfp_drugs_table
)

Arguments

input_table

A character string specifying a dataframe or path to the AMRFinderPlus results table (TSV format).

sample_col

A character string specifying the column that identifies samples in the dataset (default "Name").

element_symbol_col

Optional character string specifying the column containing gene or element symbols if non-standard column names are used.

element_type_col

Optional character string specifying the column indicating element type (e.g. AMR).

element_subtype_col

Character string specifying the column used to detect mutation subtypes.

method_col

Character string specifying the AMRFinderPlus method column.

node_col

Character string specifying the hierarchy node column.

subclass_col

Character string specifying the AMRFinderPlus subclass column.

class_col

Character string specifying the AMRFinderPlus class column.

amrfp_drugs

A tibble containing a reference table mapping AMRFinderPlus subclasses (AMRFP_Subclass) to standardised drug classes (drug_class). Defaults to amrfp_drugs_table, which is provided internally.

Value

A data frame with the processed genotype data, with harmonised gene names, mapped drug agents, and drug classes which can be used for other functions of the ARMgen package. The output retains the original columns from the AMRFinderPlus table along with the newly mapped variables:

  • id: The sample identifier (character).

  • marker: The name of the genotype marker as it appears in the input (e.g. gyrA_S83F) (character).

  • gene: The gene identifier (character).

  • mutation: The mutation detected within the gene, converted to HGVS nomenclature syntax (e.g. Ser83Phe) (character).

  • node: The node in the NCBI reference gene hierarchy corresponding to the gene (character).

  • drug_class: Name of the antibiotic group associated with the genotype marker, compatible with AMR pkg (character).

  • drug: Name of the specific antibiotic associated with the genotype marker, compatible with AMR pkg (ab). Value NA is assigned when the markers are annotated with a class only and not a specific antibiotic.

  • variation type: Type of variation, e.g. Gene presence detected, Protein variant detected, Nucleotide variant detected, Inactivating mutation detected, Promoter variant detected. ... Other fields specific to the input file

Details

The function performs the following steps:

  • Reads the AMRFinderPlus output table.

  • Filters the data to only include AMR elements.

  • Converts gene symbols to a harmonised format.

  • Splits multiple subclass annotations into separate rows.

  • Maps AMRFinderPlus subclasses to standardised drug class names recognised by the AMR pkg. This processing ensures compatibility with downstream AMRgen analysis workflows.

Examples

if (FALSE) { # \dontrun{
# small example E. coli AMRFinderPlus data
data(ecoli_geno_raw)
ecoli_geno_raw

# import first few rows of this data frame and parse it as AMRfp data
geno <- import_amrfp(ecoli_geno_raw %>% head(n = 10), "Name")
geno
} # }