CMA (version 1.30.0)

pknnCMA: Probabilistic Nearest Neighbours

Description

Nearest neighbour variant that replaces the simple voting scheme by a weighted one (based on euclidean distances). This is also used to compute class probabilities.

For S4 class information, see pknnCMA-methods.

Usage

pknnCMA(X, y, f, learnind, beta = 1, k = 1, models=FALSE, ...)

Arguments

X

Gene expression data. Can be one of the following:

• A matrix. Rows correspond to observations, columns to variables.
• A data.frame, when f is not missing (s. below).
• An object of class ExpressionSet.

y

Class labels. Can be one of the following:

• A numeric vector.
• A factor.
• A character if X is an ExpressionSet that specifies the phenotype variable.
• missing, if X is a data.frame and a proper formula f is provided.

WARNING: The class labels will be re-coded to range from 0 to K-1, where K is the total number of different classes in the learning set.

f

A two-sided formula, if X is a data.frame. The left part correspond to class labels, the right to variables.

learnind

An index vector specifying the observations that belong to the learning set. Must not be missing for this method.

beta

Slope parameter for the logistic function which is used for the computation of class probabilities. The default value (1) need not produce reasonable results and can produce warnings.

k

Number of nearest neighbours to use.

models

a logical value indicating whether the model object shall be returned

...

Currently unused argument.

Value

cloutput.

Details

The algorithm is as follows:

• Determine the k nearest neighbours
• For each class represented among these, compute the average euclidean distance.
• The negative distances are plugged into the logistic function with parameter beta.
• Classify into the class with highest probability.

See Also

compBoostCMA, dldaCMA, ElasticNetCMA, fdaCMA, flexdaCMA, gbmCMA, knnCMA, ldaCMA, LassoCMA, nnetCMA, plrCMA, pls_ldaCMA, pls_lrCMA, pls_rfCMA, pnnCMA, qdaCMA, rfCMA, scdaCMA, shrinkldaCMA, svmCMA

Examples

### load Golub AML/ALL data
data(golub)
### extract class labels
golubY <- golub[,1]
### extract gene expression from first 10 genes
golubX <- as.matrix(golub[,-1])
### select learningset
ratio <- 2/3
set.seed(111)
learnind <- sample(length(golubY), size=floor(ratio*length(golubY)))
### run probabilistic k-nearest neighbours
result <- pknnCMA(X=golubX, y=golubY, learnind=learnind, k = 3)
### show results
show(result)
ftable(result)
plot(result)