CrossVal: Creating CrossVal objects
In CrossVal: Classes and methods for cross validation of "class prediction" with microarrays or proteomics

Description Usage Arguments Details Value Author(s) References See Also Examples

Given a model classifier and a data set, this function performs cross-valiadtion by repeatedly splitting the data into training and testing subsets in order to estimate the performance of this kind of classifer on new data.

1	CrossVal(model, data, status, frac, nLoop, verbose=TRUE)

`model`
`data`
`status`
`frac`
`nLoop`
`verbose`

The CrossVal package provides generic tools for performing cross-validation on classificaiton methods in the context of high-throughput data sets such as those produced by gene expression microarrays. In order to use a classifier with this implementaiton of cross-validation, you must first prepare a pair of functions (one for learning models from training data, and one for making predictions on test data). These functions, along with any required meta-parameters, are used to create an object of the Modeler-class. That object is then passed to the CrossVal function along with the full training data set. The full data set is then repeatedly split into its own training and test sets; you can specify the fraction to be used for training and the number of iterations. The result is a detailed look at the accuracy, sensitivity, specificity, and positive and negative predictive value of the model, as estimated by cross-validation.

An object of the CrossVal-class.

Kevin R. Coombes krcoombes@mdanderson.org

See the manual page for the CrossVal-package for a list of related references.

See the manual page for the CrossVal-package for a list of classifiers that have been adapted to work with this cross-validation mechanism.

See CrossVal-class for a description of the slots in the object created by this function.

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function(model, data, status, frac, nLoop, verbose=TRUE) {
  if (length(status) != ncol(data)) {
    stop("The length of the status vector must match the size of the data set.")
  }
  
  temp <- balancedSplit(status, frac) # just to compute sizes
  nTrain <- sum(temp)
  nTest <- sum(!temp)

  # allocate space to hold the results
  trainOutcome <- data.frame(matrix(NA, ncol=nLoop, nrow=nTrain))
  validOutcome <- data.frame(matrix(NA, ncol=nLoop, nrow=nTest))
  trainPredict <- data.frame(matrix(NA, ncol=nLoop, nrow=nTrain))
  validPredict <- data.frame(matrix(NA, ncol=nLoop, nrow=nTest))
  extras <- list()
  
  for (i in 1:nLoop) {
    # show that we are still alive
    if(verbose) print(i)
    # split into training and test
    tr <- balancedSplit(status, frac)
    # record the true status for each split so we can get
    # statistics on the performance later
    trainOutcome[,i] <- status[tr]
    validOutcome[,i] <- status[!tr]
    # train the model
    thisModel <- learn(model, data[,tr], status[tr])
    # record anything interesting about the model
    extras[[i]] <- thisModel@extras
    # save the predictions on the training set
    trainPredict[,i] <- predict(thisModel)
    # now make the predictions using the logistic model
    validPredict[,i] <- predict(thisModel, newdata=data[, !tr])
  }
  new("CrossVal",
      nIterations=nLoop,
      trainPercent=frac,
      outcome=status,
      trainOutcome=trainOutcome,
      validOutcome=validOutcome,
      trainPredict=trainPredict,
      validPredict=validPredict,
      extras=extras)
  }