Kernels                package:macat                R Documentation

_v_a_r_i_o_u_s _k_e_r_n_e_l _f_u_n_c_t_i_o_n_s _f_o_r _c_o_m_p_u_t_a_t_i_o_n_s _i_n _M_A_C_A_T

_D_e_s_c_r_i_p_t_i_o_n:

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

_U_s_a_g_e:

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

_A_r_g_u_m_e_n_t_s:

geneLocations: Location of genes

position: Position on chromosome

  params: special kernel parameters

          _k_N_N: k = number of nearest genes

          _r_b_f: gamma = kernel width

          _b_a_s_e_P_a_i_r_D_i_s_t_a_n_c_e: distance = distance within which all genes
               are averaged 

_D_e_t_a_i_l_s:

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

_V_a_l_u_e:

     returns kernel weight for position, computed from the
     geneLocations

_A_u_t_h_o_r(_s):

     MACAT development team

_S_e_e _A_l_s_o:

     'evalScoring, compute.sliding, kernelize'

_E_x_a_m_p_l_e_s:

       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)  

