Export NCBI BioSample Antibiogram — export_ncbi

Convert AMRgen long-format AST data to an NCBI BioSample Antibiogram submission file.

Usage

export_ncbi_biosample(
  data,
  file,
  overwrite = FALSE,
  pheno_col = "pheno_provided"
)

Arguments

data: A data frame in AMRgen long format (e.g. output of import_ast() or format_ast()). Expected columns: id, drug_agent, and at least one phenotype column (see pheno_col). Optional columns: mic, disk, method, guideline, platform.
file: File path for the output file (must end in .txt or .tsv).
overwrite: Logical; overwrite an existing file? Default FALSE.
pheno_col: Character string naming the column that contains SIR interpretations (class sir). Default "pheno_provided".

Value

The formatted data frame is returned invisibly. A tab-delimited UTF-8 text file is written to file.

Details

When both mic and disk columns are present, MIC values are preferred (more precise). Disk values are only used for rows where MIC is NA.

MIC strings (e.g. "<=0.5", ">=32", "4") are split into a sign (<=, >=, <, >, or =) and a numeric value.

Antibiotic names are converted to lowercase with combination separators replaced by "-" (NCBI convention, e.g. "amoxicillin-clavulanic acid").

Examples

if (FALSE) { # \dontrun{
# Write out the ecoli_ast data to file in NCBI format
export_ncbi_biosample(ecoli_ast, "Ec_NCBI.tsv")

# Download data from EBI, then write it out to file in NCBI format
ebi_kleb_quasipneumoniae <- download_ebi(species = "Klebsiella quasipneumoniae", reformat = T)
export_ncbi_biosample(ebi_kq, "Kq_NCBI.tsv")
} # }