Uses all inputted database information on protein-protein interactions in order to create a combined PPI-network. All edges in the PPI network are checked against the cocluster correlation network to ensure existence and a non-zero weight. If either of these conditions are not met, then it will be removed from the list of PPI edges. This new, cluster filtered network is then assigned to the global namespace.
Usage
BuildClusterFilteredNetwork(
gene.cccn.edges,
stringdb.edges = NULL,
genemania.edges = NULL,
kinsub.edges = NULL,
db.filepaths = c(NULL)
)Arguments
- gene.cccn.edges
TODO
- stringdb.edges
Data frame of consisting of the network of interactions from the genes of study pulled from the STRINGdb database
- genemania.edges
GeneMANIA network of protein-protein interactions from the genes of study; defaults to NA
- kinsub.edges
TODO
- db.filepaths
A vector of paths to the additional ppi network files; defaults to an empty vector
Value
A list containing the following data structures at the given index:
All the database data.frames stringdb, genemania, and kinsub bound together in a data frame.
A version of ppi.network with only the edges that exist in gene.cccn and have non-zero weights.
Examples
Example_Output <- BuildClusterFilteredNetwork(ex_gene_cccn_edges,
ex_stringdb_edges, ex_genemania_edges)
utils::head(Example_Output[[2]])
#> source target interaction Weight
#> 1 ABL1 IRS2 experimental_transferred 3.589744
#> 2 ADAM10 ANXA2 experimental_transferred 2.600733
#> 3 ADAM10 IRS2 experimental_transferred 2.857143
#> 4 AFDN PLEKHA5 experimental 2.747253
#> 5 AHNAK LPP experimental_transferred 1.941392
#> 6 AHNAK NEDD9 experimental_transferred 3.772894