censIndLR: Conditional independence test for survival data

Description

The main task of this test is to provide a p-value PVALUE for the null hypothesis: feature 'X' is independent from 'TARGET' given a conditioning set CS. This test is based on the widely used Cox regression model (Cox, 1972).

Usage

censIndLR(target, dataset, xIndex, csIndex, dataInfo = NULL, univariateModels = NULL, 
hash = FALSE, stat_hash = NULL, pvalue_hash = NULL, robust = FALSE)

Arguments

target

A Survival object (class Surv from package survival) containing the time to event data (time) and the status indicator vector (event). View Surv documentation for more information.

dataset

A numeric matrix or data frame, in case of categorical predictors (factors), containing the variables for performing the test. Rows as samples and columns as features.

xIndex

The index of the variable whose association with the target we want to test.

csIndex

The indices of the variables to condition on.

dataInfo

list object with information on the structure of the data. Default value is NULL.

univariateModels

Fast alternative to the hash object for univariate test. List with vectors "pvalues" (p-values), "stats" (statistics) and "flags" (flag = TRUE if the test was succesful) representing the univariate association of each variable with the target. Default val

hash

A boolean variable which indicates whether (TRUE) or not (FALSE) to use the hash-based implementation of the statistics of SES. Default value is FALSE. If TRUE you have to specify the stat_hash argument and the pvalue_hash argument.

stat_hash

A hash object (hash package required) which contains the cached generated statistics of a SES run in the current dataset, using the current test.

pvalue_hash

A hash object (hash package required) which contains the cached generated p-values of a SES run in the current dataset, using the current test.

robust

A boolean variable which indicates whether (TRUE) or not (FALSE) to use a robustified version of Cox regression. Currently the robust version is not available for this test.

Value

A list including:
pvalueA numeric value that represents the generated p-value.
statA numeric value that represents the generated statistic.
flagA numeric value (control flag) which indicates whether the test was succesful (0) or not (1).
stat_hashThe current hash object used for the statistics. See argument stat_hash and details. If argument hash = FALSE this is NULL.
pvalue_hashThe current hash object used for the p-values. See argument stat_hash and details. If argument hash = FALSE this is NULL.

Details

If hash = TRUE, testIndLogistic requires the arguments 'stat_hash' and 'pvalue_hash' for the hash-based implementation of the statistic test. These hash Objects are produced or updated by each run of SES (if hash == TRUE) and they can be reused in order to speed up next runs of the current statistic test. If "SESoutput" is the output of a SES run, then these objects can be retrieved by SESoutput@hashObject$stat_hash and the SESoutput@hashObject$pvalue_hash. Important: Use these arguments only with the same dataset that was used at initialization. For all the available conditional independence tests that are currently included on the package, please see "?CondIndTests".

References

V. Lagani and I. Tsamardinos (2010). Structure-based variable selection for survival data. Bioinformatics Journal 16(15): 1887-1894. Cox,D.R. (1972) Regression models and life-tables. J. R. Stat. Soc., 34, 187-220.

Examples

Run this code

#create a survival simulated dataset
dataset <- matrix(nrow = 1000 , ncol = 100)
dataset <- apply(dataset, 1:2, function(i) runif(1, 1, 100))
dataset <- as.data.frame(dataset);
timeToEvent <- numeric(1000)
event <- numeric(1000)
ca <- numeric(1000)
for(i in 1:1000) {
  timeToEvent[i] <- dataset[i,1] + 0.5*dataset[i,30] + 2*dataset[i,65] + runif(1, 0, 1);
  event[i] <- sample( c(0, 1), 1)
  ca[i] <- runif(1, 0, timeToEvent[i]-0.5)
  if(event[i] == 0) {
    timeToEvent[i] = timeToEvent[i] - ca[i]
  }
}

require(survival)

#init the Surv object class feature
if(require(survival, quietly = TRUE)) {
  target <- Surv(time = timeToEvent, event = event)
  
  #run the censIndLR   conditional independence test
  res <- censIndLR( target, dataset, xIndex = 12, csIndex = c(35, 7, 4) )
  res
  
  #run the SES algorithm using the censIndLR conditional independence
  #test for the survival class variable
  
  #require(gRbase) #for faster computations in the internal functions
  sesObject <- SES(target, dataset, max_k = 1, threshold = 0.05, test = "censIndLR");
  #print summary of the SES output
  summary(sesObject);
  #plot the SES output
  plot(sesObject, mode = "all");
}

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