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Import and process antimicrobial phenotype data retrieved from NCBI BioSamples

Source: R/import_pheno.R
import_ncbi_biosample.Rd

This function will import antibiotic susceptibility testing (AST) data suitable for downstream use with AMRgen analysis functions. The expected input is phenotype data retrieved from NCBI BioSample database via the function download_ncbi_ast(). Note that files downloaded from the NCBI AST web browser https://www.ncbi.nlm.nih.gov/pathogens/ast are formatted differently and can be imported with the function import_ncbi_ast().

Usage

import_ncbi_biosample(
  input,
  interpret_eucast = FALSE,
  interpret_clsi = FALSE,
  interpret_ecoff = FALSE
)

Arguments

input

A string representing the input dataframe, or a path to an input file, to be processed.

interpret_eucast

A logical value (default is FALSE). If TRUE, the function will interpret the susceptibility phenotype (SIR) for each row based on the MIC or disk diffusion 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 interpret the susceptibility phenotype (SIR) for each row based on the MIC or disk diffusion 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 interpret the wildtype vs nonwildtype status for each row based on the MIC or disk diffusion values, against epidemiological cut-off (ECOFF) values. These will be reported in a new column ecoff, of class 'sir' and coded as 'R' (nonwildtype) or 'S' (wildtype).

Value

A data frame with the processed AST data, including additional columns:

Examples

if (FALSE) { # \dontrun{
# Download Klebsiella quasipneumoniae data, filter to amikacin
ast <- download_ncbi_ast(
  "Klebsiella quasipneumoniae",
  antibiotic = "amikacin"
)

# Reformat to simplify use with AMRgen functions
ast <- import_ncbi_biosample(ast, interpret_eucast = T)
} # }