pdnn.params.chiptype        package:affypdnn        R Documentation

_A _f_u_n_c_t_i_o_n _t_o _f_i_t _P_D_N_N _p_a_r_a_m_e_t_e_r_s

_D_e_s_c_r_i_p_t_i_o_n:

     A function to fit PDNN parameters that are chip-type specific

_U_s_a_g_e:

     pdnn.params.chiptype(energy.param.file, probes.file = NULL, probes.pack= NULL,
                          probes.data.frame = NULL,
                          seq.name, x.name, y.name, affyid.name, verbose = TRUE)

_A_r_g_u_m_e_n_t_s:

energy.param.file: Path to the energy data file (see details) 

probes.file: Path to the probe files (see details) 

probes.pack: Name of the probe pack (see details) 

probes.data.frame: A 'data.frame'

seq.name, x.name, y.name, affyid.name: The names of the columns in the
          data.frame from 'probes.pack' or 'probes.file' for the probe
          sequences, the X positions, the Y positions and the probe set
          ID respectively

 verbose: verbosity ('TRUE' or 'FALSE' 

_D_e_t_a_i_l_s:

     The parameters 'probes.file', 'probes.pack' and
     'probes.data.frame' are mutually exclusive. The function fits PDNN
     parameters that are specific to chip-types (hence specific to the
     probe sequences). It requires data files like the one found on Li
     Zhang's web page:
     (http://odin.mdacc.tmc.edu/~zhangli/PerfectMatch/) This should be
     computed once for all for a given chip type. Computed values for
     the chips are included in the package. This allows 'automagic' use
     of them when these chips types are used (as done in the function
     'expressopdnn').

_V_a_l_u_e:

     A list of: 

      Eg: environment. One entry per dinucleotide.

      Wg: numerical vector

      En: environment. One entry per dinucleotide.

      Wn: numerical vector

params.gene: environment. One entry per gene, each entry is is a list
          of elements Sg, Sn, xy  and gene.i

_w_a_r_n_i_n_g:

     The X and Y positions in the 'data.frame' are expected to be
     original ones in the Affymetrix files (starting at zero. They are
     offset by one within this function.

_S_e_e _A_l_s_o:

     'find.params.pdnn'

_E_x_a_m_p_l_e_s:

     if (interactive()) {
       energy.file <- system.file("exampleData", "pdnn-energy-parameter_hg-u95av2.txt", package="affypdnn")

       params.chiptype <- pdnn.params.chiptype(energy.file, probes.pack="hgu95av2probe")
     }

