geneConnector {netboxr} | R Documentation

## Generate sub-network mapping from a list of candidate genes

### 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, emliu.research@gmail.com

### 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
    )
    #

[Package netboxr version 1.0.1 Index]