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

In CMPG/signet: signet: Selection Inference in Gene NETworks

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)

CMPG/signet documentation built on Jan. 31, 2024, 12:56 a.m.