Import and process antimicrobial phenotype data exported from Sensititre instruments
Source:R/import_pheno.R
import_sensititre_ast.RdThis 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_ast(
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 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
- 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
Interpret against EUCAST breakpoints
- interpret_clsi
Interpret against CLSI breakpoints
- interpret_ecoff
Interpret against ECOFF values