Package index

Core Functions

Main functions for distribution fitting and power analysis

fit_distributions()

Fit distributions to peptide abundance data

power_analysis()

Power analysis for peptide abundance data

power_analysis(<character>) power_analysis(<default>)

Power analysis with specified distribution (aggregate mode)

power_analysis(<peppwr_fits>)

Power analysis for per-peptide mode using fitted distributions

Diagnostic Plots

Visualization functions for fits and power results

plot_density_overlay()

Plot density overlay: observed histogram with fitted density curve

plot_missingness()

Plot missingness statistics

plot_param_distribution()

Plot distribution of fitted parameters across peptidome

plot_power_heatmap()

Plot power heatmap: N x effect size grid

plot_power_vs_effect()

Plot power vs effect size at fixed N

plot_qq()

Plot QQ plots for goodness-of-fit

plot(<peppwr_fits>)

Plot method for peppwr_fits

plot(<peppwr_power>)

Plot method for peppwr_power

Simulation Functions

Functions for running power simulations

run_power_sim()

Run power simulation

run_power_sim_empirical()

Run power simulation using empirical bootstrap

run_power_sim_fdr()

Run FDR-aware power simulation for whole peptidome

run_power_sim_with_missingness()

Run power simulation with missingness

simulate_empirical()

Simulate experiment using empirical bootstrap

simulate_experiment()

Simulate an experiment with control and treatment groups

simulate_with_missingness()

Simulate experiment with realistic missingness

Missingness

Functions for handling missing data

compute_missingness()

Compute missingness statistics for a vector of values

compute_dataset_mnar()

Compute dataset-level MNAR metric

Statistical Tests

Test functions used in power simulations

test_bayes_t()

Bayes factor t-test

test_bootstrap_t()

Bootstrap-t test

test_rankprod()

Rank Products test

test_wilcoxon()

Wilcoxon rank-sum test

Classes and Methods

S3 classes and their methods

new_peppwr_fits()

Create a new peppwr_fits object

new_peppwr_power()

Create a new peppwr_power object

print(<peppwr_fits>)

Print method for peppwr_fits

print(<peppwr_power>)

Print method for peppwr_power

print(<summary.peppwr_fits>)

Print method for summary.peppwr_fits

print(<summary.peppwr_power>)

Print method for summary.peppwr_power

summary(<peppwr_fits>)

Summary method for peppwr_fits

summary(<peppwr_power>)

Summary method for peppwr_power

validate_peppwr_fits()

Validate a peppwr_fits object

validate_peppwr_power()

Validate a peppwr_power object

Utilities

Helper functions

get_distribution_preset()

Get distributions for a preset

is_count_data()

Check if data appears to be count data (non-negative integers)