SignetList-class: An S4 class to represent a list of "Signet" objects.

In signet: signet: Selection Inference in Gene NETworks

Description

An S4 class to represent a list of "Signet" objects.

Usage

## S4 method for signature 'SignetList'
initialize(.Object, list)

## S4 method for signature 'SignetList'
x[[i]]

## S4 method for signature 'SignetList,ANY,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'SignetList'
summary(object, ...)

Arguments

.Object	A SignetList object.
list	A list of Signet objects.
x	A SignetList object.
i	Index specifying elements to extract or replace.
j	Unused for SignetList objects.
...	Unused for SignetList objects.
drop	Unused for SignetList objects.
object	A SignetList object.

Value

Results of the simulated annealing run for a lisst of pathways.

A SignetList object.

A data frame containing summary statistics for each element (network and subnetwork sizes, subnetwork score, p-value, significant genes list)

Methods (by generic)

• initialize: Initialize a SignetList

• [[: Access the ith element (signet object) of the SignetList

• [: Access the ith element (signet object) of the SignetList

• summary: Summarize the SignetList.

Slots

results

A list of Signet objects.

signet documentation built on April 28, 2020, 7:54 p.m.