tool.subgraph.find: Find edges to adjacent nodes

In Mergeomics: Integrative network analysis of omics data

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)

Mergeomics documentation built on Nov. 8, 2020, 6:58 p.m.