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

Description Usage Arguments Value Methods (by generic) Slots

Description

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

Usage

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## 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)

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 Nov. 6, 2019, 8:01 a.m.