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 = 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

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 1.4.0 Index]