tool.subgraph.find {Mergeomics} | R Documentation

## Find edges to adjacent nodes

### Description

`tool.subgraph.find` finds the edge lists between given seed nodes and their neighbors

### Usage

    tool.subgraph.find(seeds, edgemap, heads, visited)

### Arguments

`seeds` | seed nodes' indices
`edgemap` | list of adjacent edge information for entire graph. `edgemap` can belong to either tails or heads.
`heads` | list of either head (destination) or tail (source) nodes of the entire graph
`visited` | flag holding already visited node indices during neighborhood searching

### Value

`neighbors` | neighbor edge lists of seed nodes (for either tails or heads)

### Note

Neighbor edge lists of the seed nodes should be obtained separately for tail and head nodes.

### Author(s)

Ville-Petteri Makinen

### Examples

    data(job_kda_analyze)
    depth <- 1
    direction <- 0
    ## Take one or multiple center nodes (seeds) to search the neighborhoods:
    ## e.g. take the first node in the graph as the seed, find its neighborhood:
    center.node = job.kda$graph$nodes[1]
    ## Convert center node (seed) names to indices:
    nodes <- job.kda$graph$nodes
    ranks <- match(center.node, nodes)
    ranks <- ranks[which(ranks > 0)]
    ## we already know that rank is 1, since we took the first node in the graph
    ## as an example:
    ranks <- as.integer(ranks)
    ## Find edges to adjacent nodes. (both up- and down-stream searches)
    visited <- ranks
    foundT <- tool.subgraph.find(ranks, job.kda$graph$tail2edge,
    job.kda$graph$heads, visited)
    foundH <- tool.subgraph.find(ranks, job.kda$graph$head2edge,
    job.kda$graph$tails, visited)

[Package Mergeomics version 1.15.0 Index]