exportGeneNets: Create gene interaction networks for all significant gene...
In C3c6e6/SetRank: Advanced Gene Set Enrichment Analysis

Creates for every gene set present in one or more gene set networks a gene interaction network. This network shows all known or predicted protein-protein interactions between all genes in the gene set. Each network is written out to a file in GraphML format, with the extension .net.xml. Additionally, a file called gene_net_styles.viz.xml is created as well. This file contains for each gene set network a Cytoscape visualisation style which can be used to overlay the original expression data on top of the gene set-specific interaction network for. See the vignette for more details.

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exportGeneNets(topTables, networks, collection, string, outDir,
  geneSetIDs = NULL, fields = c(geneID = "ENTREZID", symbol = "SYMBOL",
  logFC = "logFC", p = "adj.P.Val"))

`topTables`	A named list object containing one or more data frames. The names should be the same as those of `networks` argument. Each data frame should contain the expression analysis data used as input for the corresponding network in the `networks` arguments. They should at least contain four columns listing the NCBI Entrez Gene identifier, the gene symbol, the observed log-fold change and the (adjusted) p-value of each gene. See the description of the `fields` argument for details.
`networks`	A named list object containing one or more gene set networks as returned by the `setRankAnalysis` function, based on the data in the `topTables` argument.
`collection`	The gene set collection object used to create the gene set networks in the `networks` argument.
`string`	An igraph object containing a species-specific protein-protein interaction network from which to retrieve. You can use the SetRankTools set of scripts to generate this object for your species of interest.
`outDir`	The directory where to write the output files. If this directory doesn't exist, it will be created.
`geneSetIDs`	The list of gene set identifiers for which to create gene interaction networks. When omitted, the union of all gene sets found in the `networks` argument will be used.
`fields`	A named vector of strings specifying the column names of the data frames in the `topTables` argument.