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Import and process antimicrobial phenotype data exported from MicroScan instruments

Source: R/import_pheno.R
import_microscan_ast.Rd

This function imports antimicrobial susceptibility testing (AST) data from MicroScan instrument output files (wide CSV format) and converts it to the standardised long-format used by AMRgen. Supports English, Spanish, French, German, and Portuguese column names (auto-detected from metadata columns).

Usage

import_microscan_ast(
  input,
  sample_col = NULL,
  source = NULL,
  species = NULL,
  ab = NULL,
  instrument_guideline = NULL,
  interpret_eucast = FALSE,
  interpret_clsi = FALSE,
  interpret_ecoff = FALSE
)

Arguments

input

A dataframe or path to a CSV/TSV file containing MicroScan AST output data

sample_col

Column name for sample identifiers. Default: NULL (auto-detected from language-specific column names)

source

Optional source value to record for all data points

species

Optional species override for phenotype interpretation

ab

Optional antibiotic override for phenotype interpretation

instrument_guideline

Optional guideline used by the instrument for SIR interpretation

interpret_eucast

Interpret against EUCAST breakpoints

interpret_clsi

Interpret against CLSI breakpoints

interpret_ecoff

Interpret against ECOFF values

Value

Standardised AST data frame