SWAP.KTSP.CV: Performs k-fold cross validation.

In marchion/switchBox: Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm

Description

Partitions the data into k folds and applies SWAP.GetKTSP.TrainTestResults for each fold. Then it combines prediction votes by dividing the vote sums by the number of TSPs in each fold to produce an overall cross-validation result.

Usage

SWAP.KTSP.CV(inputMat, Groups, classes = NULL, k = 4, 
  folds = NULL, randomize = TRUE, ...)

Arguments

inputMat	is a matrix of data with rows being the features (such as gene names, if the matrix if gene expression data) and columns being the samples.
Groups	is a factor or a vector providing the phenotype class each sample belongs to. It should correspond to the order of samples given by the columns of inputMat.
classes	is a vetor of length 2 providing the two phenotype or class labels.
k	an integer giving the number of folds to use.
folds	a list containing the samples to be used in each fold; if NULL, the data will be split into k folds maintaning the proportions between the classes.
randomize	is a logical indicating whether to randomize the sample order before diving into k folds.
...	any further arguments to be passed on for k-TSP training.

Value

A list with items:

folds	A list containing the sample indices used in each fold.
cv	A list containing the classifier, training performance and testing performance for each fold.
stats	Overall cross-validation performance.
roc	ROC curve object for overall cross-validation performance.

Author(s)

Bahman Afsari [e-mail], Luigi Marchionni [e-mail], Wikum Dinalankara [e-mail]

References

See switchBox for the references.

See Also

SWAP.KTSP.LOO

Examples

### Load gene expression data
data(trainingData)
data(testingData)

require(pROC)

### perform leave one out cross-validation
result = SWAP.KTSP.CV(matTraining, trainingGroup, featureNo=100)

### print results
result$stats

marchion/switchBox documentation built on May 9, 2019, 4:07 p.m.