closest.transitive.greedy

do you want to see progress statements printed or not? Default: TRUE

verbose


	First, from the original graph $\Phi$ spurious edges are pruned via
	<code>prune.graph</code>. Then the new graph $\Phi'$ is transitively
	closed. Afterwards, the algorithms successively introduces new edges
	minimizing the distance to the original graph (defined as
	$\sum_{ij} |\Phi_{ij} - \Phi'_{ij}|$) most. After each edge
	addition the graph is transitively closed again. 


models

The package 'nem' allows to reconstruct features of pathways from the nested structure of perturbation effects. It takes as input (1.) a set of pathway components, which were perturbed, and (2.) phenotypic readout of these perturbations (e.g. gene expression, protein expression). The output is a directed graph representing the phenotypic hierarchy.

Holger Froehlich

(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies

closest.transitive.greedy function

First, from the original graph $\Phi$ spurious edges are pruned via
	<code>prune.graph</code>. Then the new graph $\Phi'$ is transitively
	closed. Afterwards, the algorithms successively introduces new edges
	minimizing the distance to the original graph (defined as
	$\sum_{ij} |\Phi_{ij} - \Phi'_{ij}|$) most. After each edge
	addition the graph is transitively closed again.

closest.transitive.greedy: Find transitively closed graph most similar to the given one

Description

Usage

Arguments

Value

See Also