AMR/reference/export_ncbi_biosample.md

Export Data Set as NCBI BioSample Antibiogram

Export Data Set as NCBI BioSample Antibiogram

Usage

export_ncbi_biosample(
  x,
  filename = paste0("biosample_", format(Sys.time(), "%Y-%m-%d-%H%M%S"), ".xlsx"),
  type = "pathogen MIC",
  columns = where(is.mic),
  save_as_xlsx = TRUE
)

Arguments

• x:

  A data set.

• filename:

  A character string specifying the file name.

• type:

  A character string specifying the type of data set, either "pathogen MIC" or "beta-lactamase MIC", see https://www.ncbi.nlm.nih.gov/biosample/docs/.