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Import and process antimicrobial phenotype data exported from Sensititre instruments

Source: R/import_pheno.R
import_sensititre_pheno.Rd

This function imports antimicrobial susceptibility testing (AST) data from Sensititre instrument output files (tab- or comma-separated, optionally UTF-16LE encoded, no header row) and converts it to the standardised long-format used by AMRgen.

Usage

import_sensititre_pheno(
  input,
  source = NULL,
  species = NULL,
  ab = NULL,
  instrument_guideline = NULL,
  id_col = 7,
  interpret_eucast = FALSE,
  interpret_clsi = FALSE,
  interpret_ecoff = FALSE
)

Arguments

input

Path to a Sensititre output text file (tab- or comma-separated)

source

Optional string value to record in the source column for all data points (e.g., dataset name or study identifier)

species

Optional string indicating a single species to use for phenotype interpretation (otherwise this is inferred per-sample from the input)

ab

Optional string indicating a single antibiotic to use for phenotype interpretation (otherwise this is inferred per-sample from the input)

instrument_guideline

Optional string indicating the guideline used by the instrument for SIR interpretation (e.g., "EUCAST 2025", "CLSI 2025"), used to record the guideline in the output file. Default: NULL

id_col

Integer. Column index (1-based) of the sample identifier. Default is 7, which corresponds to the sample accession column in standard Sensititre exports. Adjust if your file uses a different column for the sample ID (e.g. set to 2 for the plate/batch identifier column).

interpret_eucast

A logical value (default is FALSE). If TRUE, the function will re-interpret the susceptibility phenotype (SIR) for each observation based on the MIC values, against EUCAST human breakpoints. These will be reported in a new column pheno_eucast, of class sir.

interpret_clsi

A logical value (default is FALSE). If TRUE, the function will re-interpret the susceptibility phenotype (SIR) for each observation based on the MIC values, against CLSI human breakpoints. These will be reported in a new column pheno_clsi, of class sir.

interpret_ecoff

A logical value (default is FALSE). If TRUE, the function will re-interpret the wildtype vs nonwildtype status for each observation based on the MIC values, against epidemiological cut-off (ECOFF) values. These will be reported in a new column ecoff, of class sir and coded as NWT (nonwildtype) or WT (wildtype).

Value

Standardised AST data frame