| Protein mapping (-m) |
| mappingFile |
File mapping protein names to numeric ids |
| Sorting (-r) |
| FREQUENCY |
Sorting of adjacency list by frequency before building DAPG |
| ID |
Sorting by id in adjacency list before building DAPG |
|
Grouping (-f): Predicted protein complex formation (PC) using OS(Cx, Cy) > 0.8 |
| UNION |
PC = Cx ∪ Cy
|
| NONE |
Cx and Cy
|
| Graph Types (-g) |
| UNONE |
Undirected-unweighted graph |
| USYM |
Undirected-weighted graph |
|
Alternative
fobj
(-w)
|
| WEDGE |
Select the dense subgraphs with higher weighted-edge-density |
| WDEGREE |
Select the dense subgraphs with higher weighted-degree-density |
| FWEDGREE |
Select the dense subgraphs with higher weighted-edge-density of S ∪ C induced subgraph. |
| FWEDGE |
Select the dense subgraphs with higher weighted-degree-density of S ∪ C induced subgraph. |
