nearestShrunkenCentroidPredictInterface: Interface for `pamr.predict` Function from `pamr` CRAN Package

Description

Restructures variables from ClassifyR framework to be compatible with pamr.predict definition.

Usage

"nearestShrunkenCentroidPredictInterface"(trained, test, ...) "nearestShrunkenCentroidPredictInterface"(trained, test, ..., verbose = 3)

Arguments

trained

An object of class pamrtrained.

test

Either a matrix or ExpressionSet containing the test data. For a matrix, the rows are features, and the columns are samples.

...

For the function with matrix dispatch, arguments passed to the function with ExpressionSet dispatch. For the function with ExpressionSet dispatch, arguemnts passed to pamr.predict.

verbose

A number between 0 and 3 for the amount of progress messages to give. This function only prints progress messages if the value is 3.

Value

A factor of predicted classes for the test data.

Details

This function is an interface between the ClassifyR framework and pamr.predict.

Examples

Run this code

  if(require(pamr))
  {
    # Samples in one class with differential expression to other class.
    genesMatrix <- sapply(1:25, function(geneColumn) c(rnorm(100, 9, 1)))
    genesMatrix <- cbind(genesMatrix, sapply(1:25, function(geneColumn)
                                 c(rnorm(75, 9, 1), rnorm(25, 14, 1))))
    classes <- factor(rep(c("Poor", "Good"), each = 25))
    
    fit <- nearestShrunkenCentroidTrainInterface(genesMatrix[, c(1:20, 26:45)], classes[c(1:20, 26:45)])
    nearestShrunkenCentroidPredictInterface(fit, genesMatrix[, c(21:25, 46:50)])
  }