encodePhenotype

Source: R/run_Fisher_tests.R

encodePhenotype

encodePhenotype(
  df,
  susceptible_label = "Susceptible",
  resistant_label = "Resistant"
)

Arguments

df

A tibble with AMR column genome_drug.resistant_phenotype

susceptible_label

Label for "Susceptible" phenotype

resistant_label

Label for "Resistant" phenotype

Value

A list with:

  • df: the input data with AMR phenotype now encoded as integer

  • target: a binarized vector of the encoded AMR phenotypes