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pepdiff 1.0.0

Initial release of pepdiff for differential abundance analysis of PRM proteomics data.

Features

Analysis Methods

compare() - Main analysis function supporting three methods:
- GLM: Gamma GLM with emmeans for factorial designs (recommended)
- ART: Aligned Rank Transform for non-parametric analysis
- Pairwise: Direct two-group comparisons (Wilcoxon, bootstrap-t, Bayes factor, rank products)
Stratified comparisons with within parameter for analysing effects within factor levels

Data Management

read_pepdiff() - Import CSV data with flexible factor specification
combine_tech_reps() - Combine technical replicates before analysis
S3 classes pepdiff_data and pepdiff_results with print, summary, and plot methods

Diagnostics

plot_fit_diagnostics() - Four-panel diagnostic plot for assessing GLM model fit
Stored residuals and fitted values for post-hoc diagnostics
Convergence tracking for all fitted models

Visualization

plot() methods for both data and results objects
plot_volcano() - Volcano plots with customizable thresholds
plot_heatmap() - Heatmaps of significant peptides (requires ComplexHeatmap)
plot_pca() - PCA visualization of samples
plot_pvalue_hist() - P-value distribution histograms
plot_fc_distribution() - Fold change distributions
plot_missingness() - Missing data patterns
plot_distributions() - Abundance distributions by group

Companion Package

pepdiff is designed to work alongside peppwR:

peppwR: "How many samples do I need?" (power analysis)
pepdiff: "What's differentially abundant?" (analysis)