tool.subgraph {Mergeomics} | R Documentation

## Determine network neighbors for a set of nodes

### Description

`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.

### Usage

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

### Arguments

`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

### Value

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

### Author(s)

Ville-Petteri Makinen

### See Also

`tool.subgraph.search`

### Examples

    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)

[Package Mergeomics version 1.15.0 Index]