geneConnector: Generate sub-network mapping from a list of candidate genes

In netboxr: netboxr

Description

This function generates sub-network mapping from a list of candidate genes

Usage

geneConnector(
  geneList,
  networkGraph,
  directed = FALSE,
  pValueAdj = "BH",
  pValueCutoff = 0.05,
  communityMethod = "ebc",
  keepIsolatedNodes = FALSE
)

Arguments

geneList	character vector containing a list of candidate genes
networkGraph	igraph network graph object. This igraph object contains curated network information
directed	boolean value indicating whether the input network is directed or undirected (default = FALSE)
pValueAdj	string for p-value correction method c("BH", "Bonferroni") as described in the details section (default = "BH")
pValueCutoff	numeric value of p-value cutoff for linker nodes (default = 0.05)
communityMethod	string for community detection method c("ebc","lec") as described in the details section (default = "ebc")
keepIsolatedNodes	A boolean value indicating whether to keep isolated nodes in the netboxr result (default = FALSE)

Details

P-value correction methods include the Bonferroni correction ("bonferroni") or Benjamini & Hochberg ("BH"). Community detection methods include using edge betweeness score ("ebc") or using leading eigenvector method ("lec)

Value

a list of returned netboxr results

• netboxGraph: igraph object of NetBox algorithm identified network nodes and connections

• netboxCommunity: igraph object of network community assignment

• netboxOutput: data frame of NetBox algorithm identified network nodes and connections

• nodeType: data frame of node types ("candidate" or "linker") in the NetBox algorithm indentified network.

• moduleMembership: data frame of module (community) membership.

• neighborData: data frame of information of nodes directly connected to candidate gene nodes.

Author(s)

Eric Minwei Liu, [e-mail]

Examples

data(netbox2010)

sifNetwork<-netbox2010$network
graphReduced <- networkSimplify(sifNetwork,directed = FALSE) 

geneList<-as.character(netbox2010$geneList)

results<-geneConnector(geneList=geneList,networkGraph=graphReduced,
                      pValueAdj='BH',pValueCutoff=0.05,
                      communityMethod='lec',keepIsolatedNodes=FALSE)


names(results)

plot(results$netboxGraph, layout = layout_with_fr)


write.table(results$netboxOutput,
  file = "network.sif", sep = "	",
  quote = FALSE, col.names = FALSE, row.names = FALSE
)

write.table(results$neighborData,
  file = "neighborList.txt", sep = "	",
  quote = FALSE, col.names = TRUE, row.names = FALSE
)

write.table(results$moduleMembership,
  file = "memb.ebc.txt", sep = "	",
  quote = FALSE, col.names = FALSE, row.names = FALSE
)
#
write.table(results$nodeType,
  file = "nodeType.txt", sep = "	", quote = FALSE,
  col.names = FALSE, row.names = FALSE
)
#

netboxr documentation built on Nov. 8, 2020, 5:01 p.m.