kernelizeAll              package:macat              R Documentation

_S_m_o_o_t_h _e_x_p_r_e_s_s_i_o_n _d_a_t_a _f_o_r _a_l_l _c_h_r_o_m_o_s_o_m_e_s

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

     'kernelizeAll' smoothes complete expression matrix and writes the
     result into  one text file for each chromosome. These text files
     can be read into PYTHON.

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

     kernelizeAll(data, step.width = 1e+05, kernel = rbf, 
                  kernelparams = list(gamma = 1/10^13))

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

    data: MACATData Object

step.width: size of steps for kernelization 

  kernel: kernel function one of rbf, kNN, basePairDistance or your owm 

kernelparams: list of named kernel parameters 

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

     filename of the python flatfiles: 
     'kernelized_seq_chrom_<chrom>.py'  where <chrom> is the name of
     the chromosome.

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

     produces text files

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

     The MACAT Development Team

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

     'pydata',  'kernelizeToPython'

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

      ## Not run: 
       # !!! take some time !!!
       loaddatapkg("stjudem")
       kernelizeAll(stjude)
      
     ## End(Not run)

