tni2tnsPreprocess,TNI-method {RTNsurvival} | R Documentation

## Preprocessing of TNS class objects

### Description

Creates TNS class onbjects for regulons an survival data.

### Usage

    ## S4 method for signature 'TNI'
    tni2tnsPreprocess(
      tni,
      survivalData = NULL,
      regulatoryElements = NULL,
      time = 1,
      event = 2,
      endpoint = NULL,
      pAdjustMethod = "BH",
      keycovar = NULL,
      samples = NULL,
      excludeMid = FALSE
    )

### Arguments

`tni` | A TNI class, already processed with the same samples listed in the survival data.frame.
`survivalData` | A named data.frame with samples in rows and survival data in the columns (this does not need to be provided if avaibale in the 'TNI' object).
`regulatoryElements` | A character vector specifying which 'TNI' regulatory elements should be evaluated.
`time` | A numeric or character value corresponding to the column of the data.frame where the time of last observation is given.
`event` | A numeric or character value, corresponding to the columm of the data.frame where the 'event' information is given.
`endpoint` | A numeric value. It represents the cut-off point for the 'time', if any.
`pAdjustMethod` | A single character value specifying the p-value adjustment method to be used (see 'p.adjust' function for details).
`keycovar` | A character vector of 'keycovars' listed in 'survivalData' columns.
`samples` | An optional character vector listing samples to be analyzed.
`excludeMid` | A logical value. If TRUE, inconclusive dES values is not consired in the survival analysis.

### Value

A preprocessed TNS class

### See Also

`tni.preprocess` for similar preprocessing.

### Examples

    # load survival data
    data(survival.data)

    # load TNI-object
    data(stni, package = "RTN")

    # create a new TNS object
    stns <- tni2tnsPreprocess(stni, survivalData = survival.data,
            keycovar = c('Grade','Age'), time = 1, event = 2)

[Package RTNsurvival version 1.11.2 Index]