tni.get {RTN} | R Documentation

## Get information from individual slots in a TNI object.

### 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)

[Package RTN version 2.14.1 Index]