macat (version 1.46.0)

Kernels: 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 = list(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

Value

returns kernel weight for position, computed from the geneLocations

Details

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

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)