R: An S4 class to represent a pathway and the results of the...

Signet-class {signet}

R Documentation

An S4 class to represent a pathway and the results of the associated simulated annealing run.

Description

An S4 class to represent a pathway and the results of the associated simulated annealing run.

Usage

## S4 method for signature 'Signet'
show(object)

## S4 method for signature 'Signet'
summary(object)

## S4 method for signature 'Signet,missing'
plot(x, y, ...)

## S4 method for signature 'Signet'
initialize(.Object, pathway, scores, iterations)

Arguments

`object`	A signet object.
`x`	A signet object.
`y`	Omitted when plotting a Signet object.
`...`	Other graphical parameters.
`.Object`	Object to initialize.
`pathway`	Biological pathway (graphNEL object).
`scores`	Gene scores list.
`iterations`	Number of simulated annealing iterations.

Value

A plot of the simulated annealing run.

A signet object.

Methods (by generic)

show: Print the summary a Signet object
summary: Print the summary of a Signet object
plot: Plot a Signet object
initialize: Initialize a Signet object

Slots

connected_comp: A graphNEL object (biological pathway)
network: A data frame (gene IDs and scores)
SA: A data frame (information on the simulated annealing run)
subnet_score: A numeric value (subnetwork score)
aggregate_score: A numeric value (aggregate subnetwork score)
mean_score: A numeric value (average gene score in the pathway)
subnet_size: An integer value (subnetwork size)
subnet_genes: A factor (subnetwork genes)
p.value: A numeric value (empirical p-value)

[Package signet version 1.0.2 Index]