CoRegNet-class: Class coregnet - Specifying the structure of the network used...

In RemyNicolle/CoRegNet-bioc: CoRegNet : reconstruction and integrated analysis of co-regulatory networks

Description

coregnet is an S4 type class which specifies the structure containing the necessary data of a Co-Regulatory network. coregnet objects are constructed by the hLICORN function which infers a regulatory network from gene expression data. A coregnet object can also be initiliazed by a network constructed by any other reverse engeneering method as specified in the manual of the coregnet function.

Initialization

An object of type CoRegNet can be either built from a gene expression data set using the hLICORN function, using a data.frame containing a network specifying the activators and inhibitors of each gene or using an adjacency matrix (see the coregnet function).

Slots

GRN:

A data.frame with three columns, Target Gene, co-activators and co-repressors. Co-regulators are seperated by spaces.

adjacencyList:

A description of the network through a adjacency matrix.

bytf

A named list of lists. The first entry point, the names of the list, are the Transcription Factors of the network. For each TF a list with two entries, act and rep, contains the set of activated and repressed genes respectively.

bygene

A named list of lists. The first entry point, the names of the list, are the target genes of the network. For each gene a list with two entries, act and rep, contains the set of activators and repressors of the genes respectively.

coRegulators:

A data.frame specifying the set of inferred co-regulators with several measures and statistics for each pairs.

evidences:

A list containing all the added regulatory or co-regulatory evidences if any.

evidenceDescription:

A list containing all the added regulatory or co-regulatory evidences if any.

inferenceParameters:

A list of parameters of hLICORN.

Methods

Generic methods to be used with this class :

print

Prints the number of genes, transcription factors and regulatory interactions.

summary

Same as print

length

outputs the number of genes, transcription factors and regulatory interactions in the form of a numeric vector

dim

same as length

targets

Returns the set of target genes or the targets of a given list of regulators

regulators

Returns the set of regulators of the entwork or the set of regulators of a given list of genes.

activators

Same as regulators but returns only activators of a gene

repressors

Same as activtors for repressor regulators

as.list

Gets the network in the form of an adjacency list

as.data.frame

Get the network in the form of an edge list

addEvidences

Enriches the network with external regulation evidences

addCooperativeEvidences

Enriches the network with external evidence of cooperative interaction between regulators

refine

Refine the network based on a score which can take into account external regulation or co-regulation data.

regulatorInfluence

Predicts the influence of the regulators in the network. Returns a predicted regulatory activity sample by sample

fitCoregnet

Returns the fitness of the regulatory network given an expression dataset

display

Starts a shiny application to display the co-regulation graph

Author(s)

Remy Nicolle <remy.c.nicolle AT gmail.com>

See Also

hLICORN, coregnet

RemyNicolle/CoRegNet-bioc documentation built on Dec. 18, 2021, 9:57 a.m.