Description Usage Arguments Author(s)
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.
1 2 3 | 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 |
A named list object containing one or more gene set networks
as returned by the |
collection |
The gene set collection object used to create the gene set
networks in the |
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
|
fields |
A named vector of strings specifying the column names of the
data frames in the |
Cedric Simillion
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