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Import and process antimicrobial phenotype data files retrieved from the EBI AMR portal FTP site

Source: R/import_pheno.R
import_ebi_ast_ftp.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 the EBI AMR Portal FTP site either directly or via the function download_ebi(). Note that files downloaded from the EBI AMR Portal web browser are formatted differently and can be imported with the function import_ebi_ast().

Usage

import_ebi_ast_ftp(
  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 Salmonella phenotype data from EBI
pheno_salmonella <- download_ebi(genus = "Salmonella")

# reformat to simplify use with AMRgen functions
pheno_salmonella <- import_ebi_ast_ftp(pheno_salmonella)
} # }