# kernel.functions: Kernel functions In RANKS: Ranking of Nodes with Kernelized Score Functions

## Description

Compute similarities between feature vectors according to a specific kernel function

## Usage

 ```1 2 3 4 5 6 7``` ```cauchy.kernel(W, sigma = 1) laplacian.kernel(W, sigma = 1) gaussian.kernel(W, sigma = 1) inv.multiquadric.kernel(W, v = 1) identity.kernel(W, a = 1) linear.kernel(W, a = 1) poly.kernel(W, degree = 2, scale = -1, v = 0) ```

## Arguments

 `W` a numeric matrix, Rows are examples and columns are features `sigma` a real value representing the sigma parameter (def. 1) of the Cauchy, Gaussian and Laplacian kernel `v` constant factor (def. 1) of the inverse multiquadric kernel and of the polynomail kernel; for the inverse multiquadric kernel v must be larger than 0. `a` unused parameter, maintained for compatibility reasons . `degree` integer corresponding to a degree of the polynomial (def. 2) `scale` double: scaling factor of the polynomial kernel. If scale=-1 (def) scale is set to 1/ncol(W);

## Details

All the kernel matrices are computed by calling C code to speed-up the computation.

`cauchy.kernel` computes the Cauchy kernel.

`laplacian.kernel` computes the Lapalacian kernel.

`gaussian.kernel` computes the Gaussian kernel.

`inv.multiquadric.kernel` computes the inverse multiquadric kernel.

`identity.kernel` computes the identity kernel. In this case the input W represents a similarity square matrix (obtained i.e. through the Pearson correlation) between examples.

`linear.kernel` computes the linear kernel.

## Value

A kernel matrix representing the similarities between the examples (rows of W), according to a specific kernel function.

`rw.kernel-methods`

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11``` ```# computing kernels on the Tanimoto chemical structure similarity matrix library(bionetdata); data(DD.chem.data); K <- identity.kernel(DD.chem.data); K <- linear.kernel(DD.chem.data); ## Not run: K <- gaussian.kernel(DD.chem.data); K <- inv.multiquadric.kernel(DD.chem.data); K <- poly.kernel(DD.chem.data); ## End(Not run) ```

RANKS documentation built on May 29, 2017, 12:24 p.m.