kernelizeToPython           package:macat           R Documentation

_S_m_o_o_t_h _e_x_p_r_e_s_s_i_o_n _v_a_l_u_e_s _a_n_d _w_r_i_t_e _t_o _f_i_l_e

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

     Smoothes expression data for one chromosome and writes  the result
     into a text file, which can be read into PYTHON, or returns it
     without writing. 'kernelizeToPython' is the one-chromosome version
     of 'kernelizeAll'.

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

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

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

    data: MACATData Object 

   chrom: kernelize all genes that are on this chromosome 

step.width: widtrh of interploation steps 

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

kernelparams: list of named kernel parameters 

saveToFile: logical indicating wether to save as flat file or not 

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

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

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

     returns kernelized expression matrix

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

     The MACAT Development team

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

     'pydata', 'kernelizeAll'

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

       data(stjd)
       kernelized = kernelizeToPython(stjd, 3)

