rTRM (version 1.10.2)

findTRM: Indentifies a TRM associated with a target node and one or more query nodes.

Description

This the main function used to identify TRMs. It takes a graph object and use it to search in the neighborhood of a target node for query nodes that are separated a maximum distance (controlled by max.bridge parameter).

Usage

findTRM(g, target, query, method = "nsa", max.bridge = 1, extended = FALSE, strict = FALSE, type = "igraph")

Arguments

g

the network used to identify TRMs (tipically a PPI network)

target

character variable with the name of a target node.

query

character vector with the list of query nodes.

method

method to use.

max.bridge

maximum number of nodes allowed between the target and query nodes.

extended

whether to allow distance restrictions to include both target and query nodes.

strict

whether to return a single component (using decompose.graph())

type

type of graph object to return, either an "igraph" (the default) or a "graphNEL"

Value

• A network in igraph format or NULL.

Details

Currently only "first" and "nsa" methods are available. First is used for tests and returns the first neighborhood of the target node. Method "nsa" implements the TRM finding algorithm.

Examples

# load example network.
load(system.file(package = "rTRM", "extra/example.rda"))

# define target and query nodes.
target = "N6"
query = c("N7", "N12", "N28")

# find TRM:
s = findTRM(g, target = target, query = query, method = "nsa", max.bridge = 1)