Class "TNA": an S4 class for Transcriptional Network Analysis.

Description

This S4 class includes a series of methods to do enrichment, synergy, shadow and overlap analyses in transcriptional networks.

Objects from the Class

Objects can be created by calls of the form new("TNA", referenceNetwork, transcriptionalNetwork, transcriptionFactors, phenotype, hits).

Slots

referenceNetwork:

Object of class "matrix", an optional partial co-expression matrix.

transcriptionalNetwork:

Object of class "matrix", a partial co-expression matrix.

transcriptionFactors:

Object of class "char_Or_NULL", a vector of transcription factors.

phenotype:

Object of class "num_Or_int", a numeric or integer vector of phenotypes named by gene identifiers.

hits:

Object of class "character", a character vector of gene identifiers for those considered as hits.

annotation:

Object of class "data.frame", a data frame with transcriptional network annotation.

listOfReferenceRegulons:

Object of class "list", a list of regulons derived from the referenceNetwork.

listOfRegulons:

Object of class "list", a list of regulons derived from the transcriptionalNetwork (a 'regulon' is a vector of genes or potential transcription factor targets).

listOfModulators:

Object of class "list", a list of modulators derived from the tni.conditional analysis.

para:

Object of class "list", a list of parameters for transcriptional network analysis. These parameters are those listed in the functions tna.mra, tna.overlap, tna.gsea1, tna.synergy, tna.shadow and tna.gsea2.

results:

Object of class "list", a list of results (see return values in the functions tna.mra,tna.gsea1, tna.overlap, tna.synergy, tna.shadow and tna.gsea2)

summary:

Object of class "list", a list of summary information for transcriptionalNetwork, transcriptionFactors, phenotype,listOfRegulons, para, and results.

status:

Object of class "character", a character value specifying the status of the TNI object based on the available methods.

Methods

tna.mra

signature(object = "TNA"): see tna.mra

tna.overlap

signature(object = "TNA"): see tna.overlap

tna.gsea1

signature(object = "TNA"): see tna.gsea1

tna.gsea2

signature(object = "TNA"): see tna.gsea2

tna.synergy

signature(object = "TNA"): see tna.synergy

tna.shadow

signature(object = "TNA"): see tna.shadow

tna.get

signature(object = "TNA"): see tna.get

tna.graph

signature(object = "TNA"): see tna.graph

Author(s)

Mauro Castro

See Also

TNI-class. tni2tna.preprocess.

Examples

1
## see 'tni2tna.preprocess' method!

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