ClassifierBuild {MCRestimate}R Documentation

Building a classifier as a combination of preprocessing and classification method

Description

Usage

ClassifierBuild(eset,
                class.column,
                reference.class=NULL,
                classification.fun,
                variableSel.fun ="identity",
                cluster.fun ="identity",
                poss.parameters=list(),
                cross.inner=10,
                rand=123,
                information=TRUE,
                thePreprocessingMethods=c(variableSel.fun,cluster.fun))

Arguments

eset an object of class exprSet or exprSetRG
class.column a number or a character string which indicated the column of the expression set's phenodata containing the class label
reference.class a character string with the name of one class - if specified the class will form the first class and all the other classes will form the second class
classification.fun a character string which names the function that should be used for the classification
variableSel.fun character string which names the function that should be used for variable selection
cluster.fun character string which names the function that should be used for clustering the variables
thePreprocessingMethods vector of character with the names of all preprocessing functions- can be used instead of 'variableSel.fun' and 'cluster.fun' - see details
poss.parameters a list of possible values for the parameter of the classification method
cross.inner integer - the number of nearly equal sized parts the train set should be divided into
rand integer - the random number generator will be put in a reproducible state
information information - should classificator specific data be given(depends on the wrapper for the classification method)

Value

a list with the following arguments:

classifier.for.matrix
classifier.for.exprSet
parameter a list consisting of the estimated 'best' parameter for each cross-validation part
class.method string which names the function used for the classification
thePreprocessingMethods character string - name of the preprocessing functions that have been used
cross.inner number of blocks for a the inner cross-validation
information classificator specific data

Author(s)

Markus Ruschhaupt mailto:m.ruschhaupt@dkfz.de

Examples

## please have a look at the vignette of this package

[Package MCRestimate version 1.4.0 Index]