Build PPI Network

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(
  stringdb.edges,
  genemania.edges,
  kinsub.edges,
  gene.cccn.edges,
  db.filepaths = c()
)

Arguments

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

gene.cccn.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: 1 All the database data.frames stringdb, genemania, and kinsub bound together in a data.frame 2 A version of ppi.network with only the edges that exist in gene.cccn and have non-zero weights

Examples

Example_Output <- BuildClusterFilteredNetwork(ex.stringdb.edges, ex.gm.edges, "need example", "need example", "need example")
#> Warning: no non-missing arguments to max; returning -Inf
#> Error in `$<-.data.frame`(`*tmp*`, "Weight", value = numeric(0)): replacement has 0 rows, data has 241
utils::head(Example_Output)
#> Error: object 'Example_Output' not found