Plot Case-Control Power

Source: R/plot_full_wrappers.R

Sweeps one x-axis parameter and repeatedly calls cc_power() to plot case-control power. The wrapper supports both input_mode = "model_based" and input_mode = "model_free".

plot_cc_power(
  x_var,
  x_values,
  test = c("genotypes", "trend"),
  input_mode = c("model_based", "model_free"),
  compare_tests = FALSE,
  title = NULL,
  x_label = NULL,
  y_label = NULL,
  return_data = FALSE,
  ...
)

Arguments

x_var

Character. Parameter to vary on the x-axis.

x_values

Numeric vector of x-axis values.

test

One of "genotypes" or "trend".

input_mode

One of "model_based" or "model_free".

compare_tests

Logical. If TRUE, plot genotype and trend tests together and ignore test.

title

Optional character title override.

x_label

Optional x-axis label override.

y_label

Optional y-axis label override.

return_data

Logical. If TRUE, return the data frame instead of a ggplot.

...

Arguments passed to cc_power().

Value

A ggplot object, or a data frame if return_data = TRUE.

Details

Supported x_var values include fixed sample-size variables "N_case", "N_ctrl", and "N_total"; model and design variables "alpha", "prev", "pd", "R2", and "k"; locus-heterogeneity variables "pi" and "locus_het_rate"; phenotype-misclassification variables "theta", "phi", and "pheno_error_multiplier"; and genotype-misclassification variables "e", "e1", "e2", "e01", "e02", "e03", case/control differential three-parameter error rates, "geno_error_multiplier", and "diff_multiplier".

When x_var = "pheno_error_multiplier", baseline phenotype-error values are read from theta_base and phi_base, falling back to theta and phi if the baseline arguments are not supplied. When x_var = "geno_error_multiplier", baseline genotype-error values are read from e_base; e1_base and e2_base; e01_base, e02_base, and e03_base; or case/control baseline parameters for geno_misclass = "diff3p". All arguments supplied through ... remain fixed while x_var is swept. The x-axis contains x_values; the y-axis is the power returned by cc_power() for the selected genotype chi-square or trend test. With compare_tests = TRUE, both powers are drawn on the same axes. When sweeping x_var = "pi", set locus_het = TRUE. The exact pi = 0 null boundary is retained in returned and plotted data with zero NCP and power equal to alpha.

See also

cc_power, plot_cc_mssn.

Examples

g_aff <- c((1 - 0.05)^2, 2 * 0.05 * (1 - 0.05), 0.05^2)
g_unaff <- c((1 - 0.15)^2, 2 * 0.15 * (1 - 0.15), 0.15^2)

plot_cc_power(
  x_var = "phi",
  x_values = c(0, 0.02, 0.04),
  test = "genotypes",
  input_mode = "model_free",
  N_case = 250,
  alpha = 0.01,
  g1 = g_aff,
  g0 = g_unaff,
  prev = 0.05,
  pheno_misclass = TRUE,
  theta = 0,
  k = 1
)