network_overlap: network_overlap

Description Usage Arguments Value Examples

View source: R/lib_network.R

Description

network_overlap

Usage

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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")

Arguments

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")

Value

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

Examples

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## 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)

RITAN documentation built on Nov. 8, 2020, 8:16 p.m.