Plot TDT Power Sensitivity to Phenotype Misclassification

Plot TDT power vs phenotype misclassification rate (pi01), holding heterogeneity fixed.

plot_tdt_power_phenotype_misclassification(
  pd,
  prev,
  R1,
  R2,
  alpha = 0.05,
  delta_prime = 1,
  N,
  misclass_seq = seq(0, 0.15, by = 0.01),
  heter_fixed = 0,
  title = "TDT power vs misclassification (pi01)"
)

Arguments

pd

Numeric in (0,1). High-risk allele frequency at the marker.

prev

Numeric in (0,1). Disease prevalence (phi1).

R1, R2

Numeric. Genotype relative risks.

alpha

Numeric. Significance level (default 0.05).

delta_prime

Numeric. LD scale parameter (default 1).

N

Integer. Number of affected trios.

misclass_seq

Numeric vector. Sequence of misclassification rates.

heter_fixed

Numeric. Heterogeneity rate held fixed (default 0).

title

Character. Plot title.

Value

A ggplot object, returned invisibly after it is printed.

Details

The x-axis is phenotype misclassification probability \(\pi_{01}\) and the y-axis is the corresponding power from tdt_power(). N is a fixed number of affected trios; heter_fixed and all genetic-model parameters remain fixed while misclass_seq is swept.

See also

tdt_power, plot_tdt_power_locus_heterogeneity, and plot_tdt_power.

Examples

# Power sensitivity to phenotype misclassification
plot_tdt_power_phenotype_misclassification(
  N    = 600,
  pd   = 0.30,
  prev = 0.05,
  R1   = 1.5,
  R2   = 2.25,
  misclass_seq = c(0, 0.03, 0.06),
  heter_fixed  = 0
)