Understanding the Results Folder
The results folder has the following structure.The opt folder
This folder contains all the paths and networks resulting from the analysis with the selected parameters. We will offer a explanation of the files inside and how to interpret them, this will give you some ideas to run a posterior analysis with possible better results.
This group of files contain the results of the pathfinding step performed after calculate the relevance scores of each of the genes in the mutation data list. The paths define the set of edges connecting mutated genes from different populations, using the network file as topology backbone.
The relevance score mentioned previously in combination with the weight given to the edges will return the importance or weight of the path. This weight reflects the degree of belief that the path contributes to the adaptive phenotype.
Edge Cost Folders
The optimization strategy or sub-network inference step takes a subset of the paths found. These subset of paths will be used to build a sub-network consisting of multiple connected components which are parts of the same molecular pathway.
The sub-network creation is performed for each of the sweep cost values set in the parameters, manual or automatic. It also takes into account the number of repeats. The content of each folder will have a a result network reflecting the number of repeats set by the user and a "best" network which reflects the most stable network for the specified cost.
Additionally, the resulting network folder will contain the highest scored network for that cost. Note that sometimes the folder can be empty, this means that no network was found. That cost value can be skipped in a next run to have a more constrained result.
Resulting Networks Folder
Finally, this folder contains the highest scored network ready to visualize in html, it can be visualized in any html browser without internet connection. use the combination of "CTRL or CMD" keys + mouse scroll to zoom in and out (sometimes you will not see the network at first glance and zoom out is a good option)
Additionally, another formats are provided (.sif, .xgmml) to allow the offline visualization in other platforms as Cytoscape.