Loading data to be used for PropheticGranger
PropheticGranger algorithm requires gene expression data as input. An example of data to be used with PropheticGranger algorithm can be downloaded here. Cytoscape allows loading data tables by selecting Menu File->Import->Table->File.. Once a data file has been selected a new dialog is opened to allow us to select the way this data will be loaded to Cytoscape. First, we could decide whether to assign this data to an existing network or to load it as an unassigned table. Usually, the Unassigned table option will be selected. Then we should tell Cytoscape which elements have been used as delimiters so that data can be read correctly. Below, you can an image that shows how the import dialog should look if you want to import the provided data file correctly. The format of the data to be used is explained here.
Finally, PropheticGranger allows you to use network prior data to infer a network from your data. However, an id needs to be provided to map your data to a known network element. Sometimes, there might be more than one id representing a network element. This is the case for our provided data, where the HUGO ID column might contain a list of ids for a given row. Luckly, Cytoscape supports this kind of data, so you only need to tell Cytoscape that a specific column is actually a list of elements. This can be done by a right click on the column name in the Import panel. Below, you can see an image showing you the new dialog that appears and how this dialog should be set.