Power Analysis for Phosphopeptide Abundance Hypothesis Test
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Documentation for package ‘peppwR’ version 0.1.0
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 |