tool.subgraph.search: Search neighborhoods for given nodes
In Mergeomics: Integrative network analysis of omics data

Description Usage Arguments Value Author(s) Examples

tool.subgraph.search looks for both upstream and downstream neighborhoods of given seed node list for a given depth, gets the directed edge information among seed nodes and their neighbors, obtains statistics (degrees and strengths) for seed nodes.

1	tool.subgraph.search(graph, seeds, depth, direction)

`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`	seed nodes' indices
`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 seed nodes neighborhood information with 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

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 neighbors.
res <- tool.subgraph.search(job.kda$graph, ranks, depth, direction)