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)