network_overlap: network_overlap
In MTZimmer/RITAN: Rapid Integration of Term Annotation and Network resources

Description Usage Arguments Value Examples

network_overlap

network_overlap(gene_list = NA, resources = c("PID", "TFe", "dPPI", "CCSB",
  "STRING"), minStringScore = 700, minHumanNetScore = 0.4, minScore = 0,
  verbose = TRUE, dedup = TRUE, directed_net = FALSE,
  include_neighbors = FALSE, STRING_cache_directory = NA,
  STRING_species = 9606, STRING_version = "10")

`gene_list`	A list of genes to use. The function will identify edges across resources for or among these genes; identify the induced subnetwork around the gene_list.
`resources`	Name of network resource(s) to use.
`minStringScore`	If STRING is among the resources, only edges of at least the indicated score will be included.
`minHumanNetScore`	If HumanNet is among the resources, only edges of at least the indicated score will be included.
`minScore`	Same as above, but used for any other networks where "score" is provided
`verbose`	If TRUE (default), the function will update the user on what it is doing and how many edges are identified for each resource.
`dedup`	If TRUE (Default = TRUE), remove edges reported by multiple resources. The edge type will be a semi-colon delimited list of the resources that had reported the interaction.
`directed_net`	Logical indicating if the network resources should be interpreted as directed.
`include_neighbors`	Logical to include 1st neighbors of "gene_list" (genes not in gene_list, but directly connected to them) in the induced subnetwork.
`STRING_cache_directory`	A direcotry where STRING data files are cached to speed up subsequent queries; no need to re-download. If NA (the default), caches STRING data in your Rpackages directory. If "", uses a temporary directory that is cleared when the R-session closes.
`STRING_species`	Sepcies taxon ID (number) to use in searching STRING data. (Default = 9606)
`STRING_version`	Version of the STRING database (Default = "10")

Data table describing the induced subnetwork for "gene_list" across the requested resources.

## Get interactions among a list of genes from the PID: Pathway Interaction Database
require(RITANdata)
myGeneSet <- c('BRCA1','RAD51C','VAV1','HRAS','ABCC1','CYP1B1','CYP3A5')
sif <- network_overlap( myGeneSet, resources = 'PID')
print(sif)

## Not run: 
## Get the PPI network induced by genes within myGeneSet
## Use 4 seperate resources, but trim STRING to only include more confident interactions
sif <- network_overlap( myGeneSet, c('dPPI','PID','CCSB','STRING'), minStringScore = 500 )

## End(Not run)