In biodosimetry-uab/biodosetools: An R Shiny Application for Biological Dosimetry

library(biodosetools)
knitr::opts_chunk$set(
  fig.dpi = 96,
  collapse = TRUE,
  comment = "#>"
)

Load pre-calculated curve

The first step is to either load the pre-calculated curve in .rds format obtained in the dose-effect fitting module or input the curve coefficients manually. Clicking on "Preview data" will load the curve into the app and display it on the "Results" tabbed box.

knitr::include_graphics("figures/screenshot-translocations-estimate-01.png")

knitr::include_graphics("figures/screenshot-translocations-estimate-01b.png")

This step is accomplished in R by either using the results from fit() or by loading an existing .rds object via readRDS():

fit_results <- system.file("extdata", "translocations-fitting-results.rds", package = "biodosetools") %>%
  readRDS()

fit_results$fit_coeffs

Calculate genomic conversion factor

To be able to fit the equivalent full genome case data, we need to calculate the genomic conversion factor.

To do this, in the "Stain color options" box we select the sex of the individual, and the list of chromosomes and stains used for the translocation assay. Clicking on "Generate table" will show a table in the "Chromosome data" box in which we select the chromosome-stain pairs. Clicking on the "Calculate fraction" will calculate the genomic conversion factor.

knitr::include_graphics("figures/screenshot-translocations-estimate-02.png")

To calculate the genomic conversion factor in R we call the calculate_genome_factor() function:

genome_factor <- calculate_genome_factor(
  dna_table = dna_content_fractions_morton,
  chromosome = c(1, 2, 3, 4, 5, 6),
  color = c("Red", "Red", "Green", "Red", "Green", "Green"),
  sex = "male"
)

genome_factor

Input case data

Next we can choose to either load the case data from a file (supported formats are .csv, .dat, and .txt) or to input the data manually. If needed, the user can select to use confounders (either using Sigurdson's method, or by inputting the translocation frequency per cell). Once the table is generated and filled, the "Calculate parameters" button will calculate the total number of cells ($N$), total number of aberrations ($X$), as well as mean ($\bar{F}{p}$), standard error ($\sigma{p}$), dispersion index ($\sigma^{2}/\bar{y}$), $u$-value, expected translocation rate ($X_{c}$), full genome mean ($\bar{F}{g}$), and full genome error ($\sigma{g}$).

knitr::include_graphics("figures/screenshot-translocations-estimate-03.png")

This step is accomplished in R by calling the calculate_aberr_table() function:

case_data <- data.frame(
  C0 = 288, C1 = 52, C2 = 9, C3 = 1
) %>%
  calculate_aberr_table(
    type = "case",
    assessment_u = 1,
    aberr_module = "translocations"
  ) %>%
  dplyr::mutate(
    Xc = calculate_trans_rate_sigurdson(
      cells = N,
      genome_factor = genome_factor,
      age_value = 30,
      smoker_bool = TRUE
    ),
    Fg = (X - Xc) / (N * genome_factor),
    Fg_err = Fp_err / sqrt(genome_factor)
  )

case_data

Perform dose estimation

The final step is to select the dose estimation options. In the "Dose estimation options" box we can select type of exposure (acute or protracted), type of assessment (whole-body or partial-body), and error methods for each type of assessment.

knitr::include_graphics("figures/screenshot-translocations-estimate-04.png")

knitr::include_graphics("figures/screenshot-translocations-estimate-05.png")

To perform the dose estimation in R we can call the adequate estimate_*() functions. In this example, we will use estimate_whole_body_delta(). First of all, however, we will need to load the fit coefficients and variance-covariance matrix:

fit_coeffs <- fit_results[["fit_coeffs"]]
fit_var_cov_mat <- fit_results[["fit_var_cov_mat"]]

Since we have a protracted exposure, we need to calculate the value of $G(x)$:

protracted_g_value <- protracted_g_function(
  time = 0.5,
  time_0 = 2
)

protracted_g_value

results_whole_delta <- estimate_whole_body_delta(
  case_data,
  fit_coeffs,
  fit_var_cov_mat,
  conf_int = 0.95,
  protracted_g_value,
  aberr_module = "translocations"
)

To visualise the estimated doses, we call the plot_estimated_dose_curve() function:

r. The grey shading indicates the uncertainties associated with the calibration curve."} plot_estimated_dose_curve( est_doses = list(whole = results_whole_delta), fit_coeffs, fit_var_cov_mat, protracted_g_value, conf_int_curve = 0.95, aberr_name = "Translocations" )

biodosimetry-uab/biodosetools documentation built on Jan. 26, 2024, 5:36 p.m.