tool.subgraph: Determine network neighbors for a set of nodes
In Mergeomics: Integrative network analysis of omics data

Description Usage Arguments Value Author(s) See Also Examples

tool.subgraph finds the sub-network, i.e. neighborhood, for a given seed node list with a specified depth. It also provides graph statistics (degrees and strengths) for seed nodes.

1	tool.subgraph(graph, seeds, depth = 1, direction = 0)

`graph`	a datalist including following components: nodes: N-element array of node names tails: K-element array of node indices heads: K-element array of node indices weights: K-element array of edge weights tail2edge: N-element list of adjacent edge indices head2edge: N-element list of adjacent edge indices outstats: N-row data frame of out-degree node statistics instats: N-row data frame of in-degree node statistics stats: N-row data frame of node statistics
`seeds`	list of seed node names
`depth`	the maximum number of links to connect neighbors
`direction`	sets the directionality: use a negative value for dowstream, positive for upstream or zero for undirected

a data list including following components:

`RANK`	indices of neighboring nodes (including seeds)
`LEVEL`	number of edges away from seed
`STRENG`	sum of adjacent edge weights within neighborhood
`DEGREE`	number of adjacent edges within neighborhood

Ville-Petteri Makinen

tool.subgraph.search

data(job_kda_analyze)
## take the first node in the graph as the seed, find its neighborhood:
center.node = job.kda$graph$nodes[1]
subnet = tool.subgraph(job.kda$graph, center.node, depth=1, direction=0)