findTRM {rTRM} | R Documentation

## 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"

### 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.

### Value

A network in igraph format or NULL.

### Author(s)

Diego Diez

### 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)

[Package rTRM version 1.30.0 Index]