tool.subgraph.search: Search neighborhoods for given nodes

In zeynebkurtUCLA/Mergeomics: Integrative network analysis of omics data

Description

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.

Usage

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

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	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

Value

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

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

zeynebkurtUCLA/Mergeomics documentation built on May 14, 2019, 1:59 a.m.