getProbeDataAffy         package:matchprobes         R Documentation

_R_e_a_d _a _d_a_t_a _f_i_l_e _d_e_s_c_r_i_b_i_n_g _t_h_e _p_r_o_b_e _s_e_q_u_e_n_c_e_s _o_n _a_n _A_f_f_y_m_e_t_r_i_x _g_e_n_e_c_h_i_p

_D_e_s_c_r_i_p_t_i_o_n:

     Read a data file describing the probe sequences on an Affymetrix
     genechip

_U_s_a_g_e:

     getProbeDataAffy(arraytype, datafile, pkgname = NULL, comparewithcdf = TRUE)

_A_r_g_u_m_e_n_t_s:

arraytype: Character. Array type (e.g. 'HG-U133A')

datafile: Character with the filename of the input data file, or a
          connection (see example). If omitted a default name is
          constructed from 'arraytype' (for details you will need to
          consult this function's source code).

 pkgname: Character. Package name. If NULL the name is derived from
          'arraytype'.

comparewithcdf: Logical. If TRUE, run a consistency check against a CDF
          package of the same name (what used to be Laurent's
          "extraparanoia".)

_D_e_t_a_i_l_s:

     This function serves as an interface between the (1)
     representation of array probe information data in the packages
     that are generated by 'makeProbePackage' and (2) the vendor- and
     possibly version-specific way the data are represented in
     'datafile'.

     'datafile' is a tabulator-separated file with one row per probe,
     and column names ''Probe X'', ''Probe Y'', ''Probe Sequence'', and
     ''Probe.Set.Name''. See the vignette for an example.

_V_a_l_u_e:

     A list with three components 

 dataEnv: an environment which contains the data frame with the probe
          sequences and the other probe data.

  symVal: a named list of symbol value substitutions which can be used
          to customize the man pages. See 'createPackage'.

 pkgname: a character with the package name; will be the same as the
          function parameter 'pkgname' if it was specified; otherwise,
          the name is constructed from the parameter 'arraytype'.

     normal-bracket36bracket-normal

_S_e_e _A_l_s_o:

     makeProbePackage

_E_x_a_m_p_l_e_s:

       ## Please refer to the vignette

