tni.get {RTN} | R Documentation

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

### Description

Get information from individual slots in a TNI object and any available results from a previous analysis.

### 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', 'tnet', 'refnet', 'regulons', 'refregulons', 'regulons.and.mode', 'refregulons.and.mode', 'rowAnnotation', 'colAnnotation', 'cdt', 'cdtrev').
`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 retrieve the following types of information:

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).

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

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

cdtrev

  A data frame with the same results as retrieved above (using 'cdt'), but arranged in a different format.

### Value

Get the slot content from a `TNI-class` object.

### Author(s)

Mauro Castro

### Examples

    data(dt4rtn)

    # select 5 regulatoryElements for a quick demonstration!
    tfs4test <- dt4rtn$tfs[c("PTTG1","E2F2","FOXM1","E2F3","RUNX2")]

    ## Not run:

    rtni <- tni.constructor(expData=dt4rtn$gexp, regulatoryElements=tfs4test,
            rowAnnotation=dt4rtn$gexpIDs)
    rtni<-tni.permutation(rtni)
    rtni<-tni.bootstrap(rtni)
    rtni<-tni.dpi.filter(rtni)

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

    # get a data matrix with MI values
    # (not evaluated by 'tni.dpi.filter')
    refnet<-tni.get(rtni,what="refnet")

    # get a data matrix with MI values
    # (evaluated by 'tni.dpi.filter')
    tnet<-tni.get(rtni,what="tnet")

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

    ## End(Not run)

[Package RTN version 2.6.3 Index]