tni2tnsPreprocess,TNI-method {RTNsurvival} | R Documentation |
Creates TNS class onbjects for regulons an survival data.
## 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 )
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. |
A preprocessed TNS class
tni.preprocess
for similar
preprocessing.
# 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)