tni2tnsPreprocess-methods: Preprocessing of TNS class objects

In csgroen/RTNsurvival: Survival analysis using transcriptional networks inferred by the RTN package

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)

csgroen/RTNsurvival documentation built on May 20, 2019, 1:49 p.m.