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Get Binary Matrix of Genotype and Phenotype Data

Source: R/get_binary_matrix.R
get_binary_matrix.Rd

This function generates a binary matrix representing the resistance (R vs S/I) and nonwildtype (NWT vs WT, or R/I vs S) status for a given antibiotic, and presence or absence of genetic markers related to one or more specified drug classes. It takes as input separate tables for genotype and phenotype data, matches these according to a common identifier (either specified by column names or assuming the first column contains the ID), and filters the data according to the specified antibiotic and drug class criteria before creating a binary matrix. Suitable input files can be generated using import_ast() to import phenotype data, and import_amrfp() to import genotype data from AMRFinderPlus.

Usage

get_binary_matrix(
  geno_table,
  pheno_table,
  antibiotic,
  drug_class_list = NULL,
  keep_SIR = TRUE,
  keep_assay_values = FALSE,
  keep_assay_values_from = c("mic", "disk"),
  geno_sample_col = NULL,
  pheno_sample_col = NULL,
  sir_col = "pheno_clsi",
  ecoff_col = "ecoff",
  marker_col = "marker",
  most_resistant = TRUE
)

Arguments

geno_table

A data frame containing genotype data, in long form with one row per sample and genetic marker. Expected format is that output by import_amrfp() and must include a column labeled drug_class (indicating the antibiotic class associated with each marker), in addition to a column indicating the marker (column name specified via marker_col) and a column for sample identifiers (specified via geno_sample_col, otherwise it is assumed the first column contains identifiers).

pheno_table

A data frame containing phenotype data, in long form with one row per sample, drug and assay result. Expected format is that output by import_ast() and must include a column drug_agent (indicating the drug agent, interpretable as AMR pkg class ab), in addition to a column for sample identifiers (specified via pheno_sample_col, otherwise it is assumed the first column contains identifiers), a column with the resistance interpretation (S/I/R, specified via sir_col), and optionally a column with the ECOFF interpretation (WT/NWT or S/R, specified via ecoff_col).

antibiotic

A character string specifying the antibiotic of interest to filter phenotype data. The value must match one of the entries in the drug_agent column of pheno_table or be coercible to a match using AMR::as.ab.

drug_class_list

A character vector (optional) of drug classes to filter genotype data for markers related to the specified antibiotic. Markers in geno_table will be filtered based on whether their drug_class matches any value in this list. If not provided, the AMR pkg is used to check what class name/s are associated with the antibiotic and uses those (these are printed to screen so the user can see what is being filtered).

keep_SIR

A logical indicating whether to retain the full S/I/R phenotype column in the output. Defaults to TRUE.

keep_assay_values

A logical indicating whether to include columns with the raw phenotype assay data. Assumes there are columns labelled "mic" and "disk"; these will be added to the output table if present. Defaults to FALSE.

keep_assay_values_from

A character vector specifying which assay values (e.g., "mic", "disk") to retain if keep_assay_values is TRUE. Defaults to c("mic", "disk").

geno_sample_col

A character string (optional) specifying the column name in geno_table containing sample identifiers. Defaults to NULL, in which case it is assumed the first column contains identifiers.

pheno_sample_col

A character string (optional) specifying the column name in pheno_table containing sample identifiers. Defaults to NULL, in which case it is assumed the first column contains identifiers.

sir_col

A character string specifying the column name in pheno_table that contains the resistance interpretation (SIR) data. The values should be "S", "I", "R" or otherwise interpretable by AMR::as.sir(). If not provided, the first column prefixed with "phenotype*" will be used if present, otherwise an error is thrown. Only used if binary_matrix not provided.

ecoff_col

A character string specifying the column name in pheno_table that contains the ECOFF interpretation of phenotype. The values should be interpretable as "WT" (wildtype) and "NWT" (nonwildtype), or "S" / "I" / "R". Default "ecoff.

marker_col

A character string specifying the column name in geno_table containing the marker identifiers. Defaults to "marker".

most_resistant

A logical indicating whether, when multiple phenotype entries are present for the same sample and drug, the most resistant should be kept (otherwise the least resistant is kept). Default is TRUE.

Value

A data frame where each row represents a sample, and each column represents a genetic marker related to the specified antibiotic's drug class. The binary values in the matrix indicate the presence (1) or absence (0) of each marker for each sample, along with resistance status columns for the specified antibiotic: R for resistant (defined from sir_col, 1=R, 0=I/S) and NWT for nonwildtype (defined by ecoff_col if provided: 1=NWT, 0=WT; otherwise defined from sir_col: 1=I/R, 0=S).

Details

This function performs several steps:

  • Verifies that the pheno_table contains a drug_agent column and converts it to class ab if necessary.

  • Filters the pheno_table to retain data related to the specified antibiotic.

  • Checks that the geno_table contains markers associated with the specified drug class(es).

  • Matches sample identifiers between geno_table and pheno_table.

  • Extracts and transforms the phenotype data into a binary format indicating resistance and NWT status.

  • Constructs a binary matrix for genotype data, with each column representing a genetic marker.

  • Returns a single matrix with sample identifiers plus binary variables for each phenotype and genetic marker.

See also

compare_geno_pheno_id, as.ab, as.sir, ab_name

Examples

if (FALSE) { # \dontrun{
# Import example E. coli AMRFinderPlus data from AllTheBacteria
ecoli_geno <- import_amrfp(ecoli_geno_raw, "Name")
geno_pheno_cip <- get_binary_matrix(
  ecoli_geno,
  ecoli_ast,
  antibiotic = "Ciprofloxacin",
  drug_class_list = c("Quinolones"),
  sir_col = "pheno_clsi"
)
geno_pheno_cip <- get_binary_matrix(
  ecoli_geno,
  ecoli_ast,
  antibiotic = "Ciprofloxacin",
  drug_class_list = c("Quinolones"),
  sir_col = "Resistance phenotype",
  keep_assay_values = TRUE
)
} # }