Plot MSSN Sensitivity for Sequencing Designs

Source: R/ngs_plots.R

Plots analytic minimum sample size necessary (MSSN) against equal fixed sequencing coverage for either a case-control sequencing trend design or a TDT1-NGS design. Calculations delegate to the corresponding public MSSN API.

plot_ngs_mssn(
  design = c("cc", "tdt"),
  coverage,
  seq_error,
  return_data = FALSE,
  ...
)

Arguments

design

Either "cc" for cc_ngs_mssn() or "tdt" for tdt_ngs_mssn().

coverage

Non-empty numeric vector of integer fixed sequencing depths. TDT1-NGS requires coverage of at least 2.

seq_error

Non-empty numeric vector of symmetric per-read sequencing error probabilities in \([0,0.5)\). Multiple values produce separate curves.

return_data

Logical. If TRUE, return the exact plotting data rather than a ggplot object.

...

Fixed arguments passed to cc_ngs_mssn() or tdt_ngs_mssn(). For case-control designs, locus_het = TRUE permits a vector of pi values. TDT1-NGS accepts a fixed locus_het and heter_rate through ...; its public convention is heter_rate = 1 - pi.

Value

A ggplot object with exact results in plot$data, or a data frame when return_data = TRUE.

Details

The primary case-control y-axis is required cases; returned plot data also retain required controls, total MSSN, and achieved power. The primary TDT1-NGS y-axis is required complete trios; returned data also retain total individuals and achieved power.

At the case-control exact-null boundary pi = 0, no finite MSSN exists when requested power exceeds alpha. The row is retained with MSSN and achieved power set to NA, finite_mssn = FALSE, and status "no finite MSSN". No artificial finite value is plotted. Only this expected scientific condition is converted; invalid inputs and unexpected calculation errors propagate unchanged.

Coverage is fixed and equal for the relevant study members. These plots do not model variable/BGE coverage distributions, cost optimization, or sample-specific depth. They use no simulation.

Examples

plot_ngs_mssn(
  design = "tdt", coverage = c(4, 12, 20), seq_error = 0.005,
  power = 0.80, pd = 0.325, R1 = 1.2, alpha = 5e-8,
  verbose = FALSE
)
#> Ignoring unknown labels:
#> • colour : "Design"
#> • linetype : "Design"