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