nearestShrunkenCentroidTrainInterface: Interface for `pamr.train` Function from `pamr` CRAN Package

Description

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

Usage

"nearestShrunkenCentroidTrainInterface"(expression, classes, ...) "nearestShrunkenCentroidTrainInterface"(expression, ..., verbose = 3)

Arguments

expression

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

classes

A vector of class labels.

...

Extra arguments passed to pamr.train.

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 list with elements as described in pamr.train.

Details

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

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))
    
    nearestShrunkenCentroidTrainInterface(genesMatrix, classes)
  }