Plot TDT MSSN Sensitivity to Phenotype Misclassification

Plot required number of trios vs misclassification rate (pi01), holding heterogeneity fixed.

plot_tdt_mssn_phenotype_misclassification(
  pd,
  prev,
  R1,
  R2,
  alpha = 0.05,
  delta_prime = 1,
  target_power,
  misclass_seq = seq(0, 0.15, by = 0.01),
  heter_fixed = 0,
  title = "Required trios vs misclassification (pi01)"
)

Arguments

pd

Disease allele frequency.

prev

Disease prevalence.

R1

Genotype relative risk for heterozygotes.

R2

Genotype relative risk for risk homozygotes.

alpha

Significance level.

delta_prime

Linkage disequilibrium scaling parameter.

target_power

Numeric. Desired power for sample size calculation.

misclass_seq

Numeric vector. Sequence of misclassification rates.

heter_fixed

Numeric. Heterogeneity rate held fixed (default 0). (Other params same meaning as in plot_tdt_power_phenotype_misclassification.)

title

Plot title.

Value

A ggplot object, returned invisibly after it is printed.

Details

The x-axis is phenotype misclassification probability \(\pi_{01}\). The y-axis is MSSN, the required number of affected trios returned by tdt_mssn() for fixed target_power. heter_fixed and all genetic-model parameters remain fixed.

See also

tdt_mssn, plot_tdt_mssn_locus_heterogeneity, and plot_tdt_mssn.

Examples

# Required sample size sensitivity to phenotype misclassification
plot_tdt_mssn_phenotype_misclassification(
  target_power = 0.80,
  pd   = 0.30,
  prev = 0.05,
  R1   = 1.5,
  R2   = 2.25,
  misclass_seq = c(0, 0.03, 0.06),
  heter_fixed  = 0
)