Table 2. prolfqua Functions That Can Be Used to Fit Various Models.
| prolfqua functions | model |
|---|---|
| strategy_lm, Contrasts | linear modeling of peptide or protein abundances and group difference estimation |
| strategy_lmer, Contrasts | mixed effect modeling of peptide or protein abundances and group differences estimation |
| ContrastsMissing | group difference estimation when no observations in one of the groups |
| ContrastsROPECA | estimating group differences for proteins by summarizing peptide differences |
| ContrastsModerated | empirical Bayes variance shrinkage for group difference estimates (limma) |
| runSaint, ContrastsSAINTexpress | protein interaction scoring (SAINTexpress) |
| strategy_proDA,a ContrastsProDA | adapter to the probabilistic dropout model implemented in proDA |
a
In development.