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Import and Process ABRicate Results

Source: R/import_geno.R
import_abricate.Rd

This function imports and processes ABRicate results, extracting antimicrobial resistance (AMR) elements and mapping them to standardised antibiotic names and drug classes. Currently supports results generated using the ResFinder database.

Usage

import_abricate(
  input_table,
  sample_col = "FILE",
  gene_col = "GENE",
  product_col = "PRODUCT",
  ab_col = "RESISTANCE",
  db = "resfinder"
)

Arguments

input_table

A character string specifying a dataframe or path to the ABRicate results table.

sample_col

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

gene_col

A character string specifying the column that identifies gene symbols in the dataset (default "GENE").

product_col

A character string specifying the column that identifies product names in the dataset (default "PRODUCT").

ab_col

A character string specifying the column that identifies which drug/s each detected gene is associated with (default "RESISTANCE").

db

A character string specifying which AMR gene database ABRicate was run with (default "resfinder"; "ncbi" is also supported).

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:

  • id: The sample identifier (character).

  • marker: The name of the genotype marker, as it appears in the GENE column of the input file (character).

  • gene: The name of the gene product, as it appears in the PRODUCT column of the input file (character).

  • drug_class: Name of the antibiotic group associated with the genotype marker, compatible with AMR pkg, parsed from the RESISTANCE column of the input file which depends on the database that ABRicate was run with (character).

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

  • variation type: Type of variation, i.e. Gene presence detected, as ABRicate only detects presence/absence of genes in the query database. ... Other fields specific to the input file

Details

The function performs the following steps:

  • Reads the ABRicate output table via the internal process_input function.

  • Standardises the sample column name 'id'.

  • Assigns standardised column names for genes, markers, and sets variation type to "Gene presence detected".

  • Splits multiple resistance annotations (separated by semicolons) into separate rows.

  • Converts drug agent names and classes to terms recognised by the AMR package.

Examples

if (FALSE) { # \dontrun{
geno_table <- import_abricate("path/to/abricate_resfinder.tsv")

geno_table2 <- import_abricate("path/to/abricate_ncbi.tsv", db = "ncbi")
} # }