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Import and Process AMRFinderPlus Results

Source: R/import_amrfp.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 (AFP_Subclass) to standardised drug agents (drug_agent) and drug classes (drug_class). Defaults to amrfp_drugs_table, which is provided internally.

Value

A tibble containing the processed AMR elements, with harmonised gene names, mapped drug agents, and drug classes. The output retains the original columns from the AMRFinderPlus table along with the newly mapped variables.

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 agent and drug class names using amrfp_drugs.

  • Converts drug agent names to the "ab" class from the AMR package. This processing ensures compatibility with downstream AMR 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
} # }