KTSP.Classify: Function to classify samples using a KTSP classifier.

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

Description

KTSP.Classify classifies new test samples using KTSP coming out of the function KTSP.Train. This function was used in Marchionni et al, 2013, BMC Genomics, and it is maintained only for backward compatibility. It has been replaced by SWAP.KTSP.Classify.

Usage

  KTSP.Classify(data, classifier, combineFunc)

Arguments

data	the test data: a matrix in which the rows represent the genes and the columns the samples.
classifier	The output of KTSP.Train, a KTSP classifier.
combineFunc	A user defined function to combine the predictions of the individual K TSPs. If missing the consensus classification among the majority of the TSPs will be used.

Author(s)

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

References

See switchBox for the references.

See Also

KTSP.Train, SWAP.KTSP.Classify,

Examples

##################################################
### Load gene expression data for the training set
data(trainingData)

### Turn into a numeric vector with values equal to 0 and 1
trainingGroupNum <- as.numeric(trainingGroup) - 1

### Show group variable for the TRAINING set
table(trainingGroupNum)


##################################################
### Train a classifier using default filtering function based on the Wilcoxon test
classifier <- KTSP.Train(matTraining, trainingGroupNum, n=8)

### Show the classifier
classifier


##################################################
### Testing on new data

### Load the example data for the TEST set
data(testingData)

### Turn into a numeric vector with values equal to 0 and 1
testingGroupNum <- as.numeric(testingGroup) - 1

### Show group variable for the TEST set
table(testingGroupNum)

### Apply the classifier to one sample of the TEST set using
### sum of votes grearter than 2
testPrediction <- KTSP.Classify(matTesting, classifier,
     combineFunc = function(x) sum(x) < 2.5)

### Show prediction
table(testPrediction, testingGroupNum)

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