tni.get: Get information from individual slots in a TNI object.

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

Description

Get available results from individual slots in a TNI object.

Usage

tni.get(object, what="summary", order=TRUE, ntop=NULL, reportNames=TRUE, 
idkey=NULL)

Arguments

object	an object of class TNI-class.
what	a single character value specifying which information should be retrieved from the slots. Options: 'summary', 'status', 'para', 'gexp','regulatoryElements', 'targetElements', 'modulators', 'tnet', 'refnet', 'regulons', 'refregulons', 'regulons.and.mode', 'refregulons.and.mode', 'rowAnnotation', 'colAnnotation', 'cdt.list', 'cdt.table', 'regulonSize','regulonActivity'.
order	a single logical value specifying whether or not the output data should be ordered by significance. Valid only for 'cdt' option.
ntop	a single integer value specifying to select how many results of top significance from 'cdt' option.
reportNames	a single logical value specifying to report regulators with 'names' (when reportNames=TRUE) or not (when reportNames=FALSE). This option takes effect on 'cdt' option if regulators are named with alternative identifiers.
idkey	an optional single character value specifying an ID name from the available 'TNI' annotation to be used as alias for data query outputs (obs. it has no effect on consolidated tables).

Details

Options for the 'what' argument:

summary

A list summarizing parameters and results available in the TNI object (see tni.regulon.summary for a summary of the network and regulons).

status

A vector indicating the status of each available method in the pipeline.

para

A list with the parameters used by each available method in the pipeline.

gexp

A gene expression matrix.

regulatoryElements

A vector of regulatory elements (e.g. transcription factors).

targetElements

A vector of target elements (e.g. TF targets).

modulators

A vector of modulators (e.g. TF modulators).

tnet

A data matrix with MI values, evaluated by the DPI filter. MI values are computed between regulators and targets, with regulators on cols and targets on rows. Note that signals (+/-) are assigned to the inferred associations in order to represent the 'mode of action', which is derived from Pearson's correlation between regulators and targets.

refnet

A data matrix with MI values (not evaluated by the DPI filter). MI values are computed between regulators and targets, with regulators on cols and targets on rows. Note that signals (+/-) are assigned to the inferred associations in order to represent the 'mode of action', which is derived from Pearson's correlation between regulators and targets.

regulons

A list with regulons extracted from the 'tnet' data matrix.

refregulons

A list with regulons extracted from the 'refnet' data matrix.

regulons.and.mode

A list with regulons extracted from the 'tnet' data matrix, including the assiged 'mode of action'.

refregulons.and.mode

A list with regulons extracted from the 'refnet' data matrix, including the assiged 'mode of action'.

rowAnnotation

A data frame with probe-to-gene annotation.

colAnnotation

A data frame with sample annotation.

cdt.table

A data frame with results from the tni.conditional analysis pipeline.

cdt.list

A list with results from the tni.conditional analysis pipeline.

regulonSize

A data frame with the number of targets annotated in each regulon.

regulonActivity

A list with results from the tni.gsea2 analysis pipeline.

Value

Get the slot content from a TNI-class object.

Author(s)

Mauro Castro

Examples

data(tniData)

## Not run: 

rtni <- tni.constructor(expData=tniData$expData, 
        regulatoryElements=c("PTTG1","E2F2","FOXM1","E2F3","RUNX2"), 
        rowAnnotation=tniData$rowAnnotation)
rtni <- tni.permutation(rtni)
rtni <- tni.bootstrap(rtni)
rtni <- tni.dpi.filter(rtni)

# check summary
tni.get(rtni, what="summary")

# get regulons
regulons <- tni.get(rtni, what = "regulons")

# get status of the pipeline
tni.get(rtni, what="status")

## End(Not run)

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