nvalidation-class: Class "nvalidation"

In cancerclass: Development and validation of diagnostic tests from high-dimensional molecular data

Description

This class of objects is returned by the function nvalidation and represents the validation of a nearest centroid predictor in a random validation protocol. Objects of this class have methods for the function plot.

Objects from the Class

Objects can be created by calls of the form new("nvalidation", ...). describe objects here

Slots

ngenes:

Numerical vector containing the numbers features that are used for classification.

method:

Character string specifying the feature selection method. Possible values are "cor", "student.test", "welch.test", "wilcoxon.test", "foldchange", "copa", "os", "ort", "shift", "throw".

dist:

Character string specifiying the method for calculation of the distance between test samples and the centroids. Possible values are "euclidean", "angle", "cor", "center".

ntrain:

The number of samples in the training set.

nrep:

The number of repetitions for each training set size.

hparam:

Hyperparameter needed for some of the feature selection methods. For methods copa, ors and os: Quantile (e.g. 0.75, 0.9, 0.95) used in order to detect outliers. For methods shift and throw: the minimum number of samples in each class after applying shift or throw.

misclass:

A list containing the total, the class1 and the class2 misclassification rates.

nselected:

Contains information, how often each of the genes was selected for a predictor.

samples:

Numeric matrix containing the classification rates for each of the samples.

classifier:

Numerical or character vector containing the class membership of the samples.

fdata:

Feature annotations inherited from the ExpressionSet.

Methods

There are three plot methods for visualization of the validation results.

See Also

nvalidate, nvalidation

Examples

showClass("nvalidation")

cancerclass documentation built on Nov. 8, 2020, 5:31 p.m.