| addReference | Add reference species | 
| addReference-method | Class '"Path2PPI"' | 
| ai | Data set to predict autophagy induction in _Podospora anserina_ | 
| getHybridNetwork | Get hybrid network of the predicted PPI | 
| getHybridNetwork-method | Class '"Path2PPI"' | 
| getPPI | Get predicted PPI | 
| getPPI-method | Class '"Path2PPI"' | 
| homologyScore | Computes homology scores | 
| human.ai.irefindex | Data set to predict autophagy induction in _Podospora anserina_ | 
| human.ai.proteins | Data set to predict autophagy induction in _Podospora anserina_ | 
| initialize-method | Class '"Path2PPI"' | 
| pa2human.ai.homologs | Data set to predict autophagy induction in _Podospora anserina_ | 
| pa2yeast.ai.homologs | Data set to predict autophagy induction in _Podospora anserina_ | 
| Path2PPI | Class '"Path2PPI"' | 
| Path2PPI-class | Class '"Path2PPI"' | 
| plot.Path2PPI | Plots the predicted PPI | 
| plot.Path2PPI-method | Class '"Path2PPI"' | 
| predictPPI | Prediction of the PPI | 
| predictPPI-method | Class '"Path2PPI"' | 
| removeReference | Remove reference species | 
| removeReference-method | Class '"Path2PPI"' | 
| show-method | Class '"Path2PPI"' | 
| showInteraction | Information about an interaction | 
| showInteraction-method | Class '"Path2PPI"' | 
| showInteraction-methods | Information about an interaction | 
| showReferences | Information about reference species | 
| showReferences-method | Class '"Path2PPI"' | 
| yeast.ai.irefindex | Data set to predict autophagy induction in _Podospora anserina_ | 
| yeast.ai.proteins | Data set to predict autophagy induction in _Podospora anserina_ |