subNetwork: Create a subGraph

In BioNet: Routines for the functional analysis of biological networks

Description

The function creates a subgraph with the nodes given in the nodeList or for these nodes including their direct neighbors.

Usage

subNetwork(nodeList, network, neighbors=c("none", "first"))

Arguments

nodeList	Character vector of nodes, contained in the subgraph.
network	Graph that is used for subgraph extraction.
neighbors	Neighborhood, that is chosen for the subgraph extraction. "none" are only the selected nodes, "first" includes the direct neighbors of the selected nodes.

Value

A graph object.

Author(s)

Marcus Dittrich

Examples

library(igraph)
el <- cbind(c("a", "b", "c", "d", "e", "f", "d"), c("b", "c", "d", "e", "f", "a", "b"))
graph <- graph.edgelist(el, directed=TRUE)

node.list <- c("a", "b", "c")
graph2 <- subNetwork(nodeList=node.list, network=graph)
## Not run: par(mfrow=c(1,2));
plotModule(graph);
plotModule(graph2)
## End(Not run)

# or in graphNEL format: 
graph3 <- igraph.to.graphNEL(graph)
graph4 <- subNetwork(nodeList=node.list, network=graph3)
graph3
graph4

Example output

Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: RBGL

Attaching package: 'igraph'

The following objects are masked from 'package:RBGL':

    bfs, dfs, transitivity

The following objects are masked from 'package:graph':

    degree, edges, intersection, union

The following objects are masked from 'package:BiocGenerics':

    normalize, path, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

A graphNEL graph with directed edges
Number of Nodes = 6 
Number of Edges = 7 
A graphNEL graph with directed edges
Number of Nodes = 3 
Number of Edges = 2 

BioNet documentation built on Nov. 8, 2020, 5:48 p.m.