mirix_antibiotic: Calculate antibiotic-specific MiRIx values

In tuv292/abx_idx: Modeling the Susceptibility of a Bacterial Community to Antibiotics

Calculate antibiotic-specific MiRIx values

Description

Calculate antibiotic-specific MiRIx values

Usage

mirix_vancomycin(
  abundance,
  lineage,
  replace_zero = 1e-04,
  antibiotic_db = whatbacteria::taxon_susceptibility,
  phenotype_db = whatbacteria::taxon_phenotypes
)

mirix_doxycycline(
  abundance,
  lineage,
  replace_zero = 1e-04,
  antibiotic_db = whatbacteria::taxon_susceptibility
)

mirix_amoxicillin(
  abundance,
  lineage,
  replace_zero = 1e-04,
  antibiotic_db = whatbacteria::taxon_susceptibility
)

mirix_metronidazole(
  abundance,
  lineage,
  replace_zero = 1e-04,
  phenotype_db = whatbacteria::taxon_phenotypes
)

mirix_ciprofloxacin(
  abundance,
  lineage,
  replace_zero = 1e-04,
  phenotype_db = whatbacteria::taxon_phenotypes
)

mirix_gentamicin(
  abundance,
  lineage,
  replace_zero = 1e-04,
  antibiotic_db = whatbacteria::taxon_susceptibility,
  phenotype_db = whatbacteria::taxon_phenotypes
)

Arguments

abundance	A vector of taxon abundances in a sample
lineage	A character vector of taxonomic assignments or lineages
replace_zero	Zero-replacement value. If the numerator or denominator is smaller than this value, they will be replaced with the number here. This number should generally be slightly less than the minimum measurement that could be acquired with the method used. For count data, a value of 0.5 is typical. For relative abundances, a number that is slightly lower than the lowest relative abundance will work.
antibiotic_db	A data frame with columns named "taxon", "rank", "antibiotic", and "value"
phenotype_db	A data frame with columns named "taxon", "rank", "gram_stain", and "aerobic_status"

Examples

h22 <- weiss2021_data[weiss2021_data$sample_id %in% "Healthy.22",]
mirix_vancomycin(h22$proportion, h22$lineage)

tuv292/abx_idx documentation built on June 28, 2024, 11:31 p.m.