Mergeomics (version 1.0.0)

tool.subgraph.find: 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)

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)