kernels: various kernel functions for computations in MACAT
In macat: MicroArray Chromosome Analysis Tool

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

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

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

returns kernel weight for position, computed from the geneLocations

MACAT development team

evalScoring, compute.sliding, kernelize

  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)