R: Power Analysis for Phosphopeptide Abundance Hypothesis Test

# Power Analysis for Phosphopeptide Abundance Hypothesis Test

## Documentation for package ‘peppwR’ version 0.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

compute_dataset_mnar | Compute dataset-level MNAR metric
compute_missingness | Compute missingness statistics for a vector of values
fit_distributions | Fit distributions to peptide abundance data
get_distribution_preset | Get distributions for a preset
is_count_data | Check if data appears to be count data (non-negative integers)
new_peppwr_fits | Create a new peppwr_fits object
new_peppwr_power | Create a new peppwr_power object
plot.peppwr_fits | Plot method for peppwr_fits
plot.peppwr_power | Plot method for peppwr_power
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
power_analysis | Power analysis for peptide abundance data
power_analysis.character | Power analysis with specified distribution (aggregate mode)
power_analysis.default | Power analysis with specified distribution (aggregate mode)
power_analysis.peppwr_fits | Power analysis for per-peptide mode using fitted distributions
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
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
summary.peppwr_fits | Summary method for peppwr_fits
summary.peppwr_power | Summary method for peppwr_power
test_bayes_t | Bayes factor t-test
test_bootstrap_t | Bootstrap-t test
test_rankprod | Rank Products test
test_wilcoxon | Wilcoxon rank-sum test
validate_peppwr_fits | Validate a peppwr_fits object
validate_peppwr_power | Validate a peppwr_power object