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AMR Logistic Regression Analysis

Source: R/plot_estimates.R
amr_logistic.Rd

Performs logistic regression to analyze the relationship between genetic markers and phenotype (R, and NWT) for a specified antibiotic.

Usage

amr_logistic(
  geno_table,
  pheno_table,
  antibiotic,
  drug_class_list,
  geno_sample_col = NULL,
  pheno_sample_col = NULL,
  sir_col = "pheno",
  ecoff_col = "ecoff",
  maf = 10,
  glm = FALSE,
  single_plot = TRUE,
  colors = c("maroon", "blue4"),
  axis_label_size = 9
)

Arguments

geno_table

A data frame containing the genotype data.

pheno_table

A data frame containing the phenotypic data.

antibiotic

A character string specifying the antibiotic to model using logistic regression.

drug_class_list

A vector of drug class names. Used to subset the relevant markers for analysis.

geno_sample_col

(Optional) A character string specifying the column in geno_table that identifies the sample IDs. Defaults to NULL.

pheno_sample_col

(Optional) A character string specifying the column in pheno_table that identifies the sample IDs. Defaults to NULL.

sir_col

(Optional) A character string specifying the column in pheno_table that contains the phenotype values (e.g., resistance/susceptibility). Defaults to "pheno".

ecoff_col

(Optional) A character string specifying the column in pheno_table containing the ECOFF (epidemiological cutoff) values. Defaults to "ecoff".

maf

(Optional) An integer specifying the minimum allele frequency (MAF) threshold. Markers with a MAF lower than this value will be excluded. Defaults to 10.

glm

(Optional) Change to TRUE to fit model with glm. Otherwise fit model with logistf (default).

single_plot

(Optional) A logical value. If TRUE, a single plot is produced comparing the estimates for resistance (R) and non-resistance (NWT). Otherwise, two plots are printed side-by-side. Defaults to TRUE.

colors

(Optional) A vector of two colors, to use for R and NWT models in the plots. Defaults to c("maroon", "blue4").

axis_label_size

(Optional) A numeric value controlling the size of axis labels in the plot. Defaults to 9.

Value

A list with three components:

bin_mat

The binary matrix of genetic data and phenotypic resistance information.

modelR

The fitted logistic regression model for resistance (R).

modelNWT

The fitted logistic regression model for non-resistance (NWT).

plot

A ggplot object comparing the estimates for resistance and non-resistance with corresponding statistical significance indicators.

Examples

# Example usage of the amr_logistic function
result <- amr_logistic(geno_table = import_amrfp(ecoli_geno_raw, "Name"), 
                      pheno_table = ecoli_ast, 
                      antibiotic = "Ciprofloxacin", 
                      drug_class_list = c("Quinolones"), 
                      maf = 10)
#> Input is already a dataframe.
#> [1] "Some samples had multiple phenotype rows, taking the most resistant only"
#> [1] "Defining NWT using ecoff column provided: ecoff"
#> [1] "Fitting logistic regression models using logistf"


# To access the plot:
print(result$plot)