TNI-class: Class '"TNI"': an S4 class for Transcriptional Network...

In RTN: RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

Description

This S4 class includes a series of methods to do transcriptional network inference for high-throughput gene expression.

Slots

gexp:

Object of class "matrix", a gene expression matrix.

regulatoryElements:

Object of class "character", a vector of regulatory elements (e.g. transcription factors).

targetElements:

Object of class "character", a vector of target elements (e.g. target genes).

modulators:

Object of class "char_Or_NULL", a vector with modulator identifiers.

rowAnnotation:

Object of class "data.frame", a data frame with row annotation (e.g. probe-to-gene information).

colAnnotation:

Object of class "data.frame", a data frame with column annotation (e.g. sample information).

para:

Object of class "list", a list of parameters for transcriptional network inference. These parameters are those listed in the functions tni.permutation, tni.bootstrap and tni.dpi.filter.

results:

Object of class "list", a list of results (see the returned values in the functions tni.permutation).

summary:

Object of class "list", a list of summary information for gexp, regulatoryElements, para, and results.

status:

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

Methods

tni.preprocess

signature(object = "TNI"): see tni.preprocess

tni.permutation

signature(object = "TNI"): see tni.permutation

tni.bootstrap

signature(object = "TNI"): see tni.bootstrap

tni.dpi.filter

signature(object = "TNI"): see tni.dpi.filter

tni.conditional

signature(object = "TNI"): see tni.conditional

tni.get

signature(object = "TNI"): see tni.get

tni.graph

signature(object = "TNI"): see tni.graph

tni.gsea2

signature(object = "TNI"): see tni.gsea2

tni.area3

signature(object = "TNI"): see tni.area3

tni.regulon.summary

signature(object = "TNI"): see tni.regulon.summary

tni.prune

signature(object = "TNI"): see tni.prune

tni.replace.samples

signature(object = "TNI"): see tni.replace.samples

tni.annotate.regulons

signature(object = "TNI"): see tni.annotate.regulons

tni.annotate.samples

signature(object = "TNI"): see tni.annotate.samples

tni.overlap.genesets

signature(object = "TNI"): see tni.overlap.genesets

tni2tna.preprocess

signature(object = "TNI"): see tni2tna.preprocess

tni.sre

signature(object = "TNI"): see tni.sre

Author(s)

Mauro Castro

See Also

TNA-class

Examples

## see 'tni.constructor'!

RTN documentation built on Nov. 12, 2020, 2:02 a.m.