Kernels {macat} | R Documentation

## various kernel functions for computations in MACAT

### Description

Various Kernel functions for computations in MACAT. Normally not called by user. All kernel functions have the same arguments in the same order!!!

### Usage

    kNN(geneLocations, position, params)
    rbf(geneLocations, position, params = list((gamma=1/10^13)))
    basePairDistance(geneLocations, position, params = (distance = 1e+06)))

### Arguments

`geneLocations` | Location of genes
`position` | Position on chromosome
`params` | special kernel parameters kNN: k = number of nearest genes rbf: gamma = kernel width basePairDistance: distance = distance within which all genes are averaged

### Details

For internal use by other MACAT-functions. Not called by user.

### Value

returns kernel weight for position, computed from the geneLocations

### Author(s)

MACAT development team

### See Also

`evalScoring, compute.sliding, kernelize`

### Examples

      data(stjd)
      genes = seq(100)
      geneLocations = abs(stjd$geneLocation[genes])
      position = c(1000) # location for which you want the kernelweights
      kernelweights = rbf(as.matrix(geneLocations), as.matrix(position),
                          list(gamma=1/10e13))
      hist(kernelweights)

[Package macat version 1.2.0 Index]