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,
  excludeAttribs = NULL
)

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.

excludeAttribs

A character vector of attributes listed in the column names of the survivalData, indicating sample groups to be excluded from the survival analysis. All attributes should be binary encoded. Available attributes can be checked by running colnames(tnsGet(tns, "survivalData"))

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 1.16.0 Index]