findTRM: Indentifies a TRM associated with a target node and one or...
In rTRM: Identification of transcriptional regulatory modules from PPI networks

Description Usage Arguments Details Value Author(s) Examples

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).

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

`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"

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.

A network in igraph format or NULL.

Diego Diez

# 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)