Export NCBI BioSample Antibiogram

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

Usage

export_ncbi_pheno(
  data,
  file = NULL,
  overwrite = FALSE,
  pheno_col = "pheno_provided",
  guideline = NULL,
  vendor = NULL,
  version = NULL
)

Arguments

data

A data frame in AMRgen long format (e.g. output of import_pheno() or format_pheno()). Expected columns: id, drug, 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). If NULL (default), no file is written and the formatted data frame is returned visibly.

overwrite

Logical; overwrite an existing file? Default FALSE.

pheno_col

Character string naming the column that contains SIR interpretations (class sir). Default "pheno_provided".

guideline

Optional single value to record in testing_standard field in the output (default NULL, in which case testing_standard will be populated from the guideline field in the input file).

vendor

Optional single value to record in vendor field in the output (default NULL).

version

Optional single value to record in laboratory_typing_method_version_or_reagent field in the output (default NULL).

Value

When file is provided, the formatted data frame is returned invisibly and a tab-delimited UTF-8 file is written to file. When file = NULL, the formatted data frame is returned visibly and no file is written.

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{
# Return formatted data frame without writing a file
ncbi_df <- export_ncbi_pheno(ecoli_pheno)

# Write out the ecoli_pheno data to file in NCBI format
export_ncbi_pheno(ecoli_pheno, "Ec_NCBI.tsv")

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