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