AffySNPCNVPDInfoPkgSeed-class package:pdInfoBuilder R Documentation

_C_l_a_s_s "_A_f_f_y_S_N_P_C_N_V_P_D_I_n_f_o_P_k_g_S_e_e_d"

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

     This class represents Platform Design (PD) packages for Affymetrix
     genomewide (SNP 6.0) arrays.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form
     'new("AffySNPCNVPDInfoPkgSeed", cdfFile, csvAnnoFile, csvSeqFile,
     csvAnnoFileCnv, csvSeqFileCnv, splineParamFile, crlmmInfoFile,
     referenceDistFile, ...)'.

_S_l_o_t_s:


     '_c_d_f_F_i_l_e': Path to the CDF file for this.

     '_c_s_v_A_n_n_o_F_i_l_e': Path to the Affymetrix CSV annotation for the SNP
          probes.

     '_c_s_v_S_e_q_F_i_l_e': Path to the (SNP) probe sequence file.

     '_c_s_v_A_n_n_o_F_i_l_e_C_n_v': Path to the Affymetrix CSV annotation for the
          CNV probes.

     '_c_s_v_S_e_q_F_i_l_e_C_n_v': Path to the (CNV) probe sequence file.

     '_s_p_l_i_n_e_P_a_r_a_m_F_i_l_e': Path to the spline parameters file used to
          compute the predicted accuracy of the the genotype calls. 
          Used internally in '.predictAccuracy'.

     '_c_r_l_m_m_I_n_f_o_F_i_l_e': Path to is data file containing regions data used
          by the 'crlmm' function.

     _r_e_f_e_r_e_n_c_e_D_i_s_t_F_i_l_e Path to a reference distribution file used in
          the normalization step. This is the reference used in
          'snprma'.

     '_c_h_i_p_N_a_m_e': Name of the chip or platform

     '_m_a_n_u_f_a_c_t_u_r_e_r': chip/platform manufacturer

     '_g_e_n_o_m_e_b_u_i_l_d': The genome build this platform is based upon.

     '_p_d_I_n_f_o_O_b_j_e_c_t_N_a_m_e': Name of the R object that will be made
          available in a generated pdInfo package.

     '_g_e_o_m_e_t_r_y': Used to describe the geometry of the platform. 

     '_n_a_m_e': The name of the package.

     '_v_e_r_s_i_o_n': A character vector giving the version number of the
          package.

     '_l_i_c_e_n_s_e': The license of the package

     '_a_u_t_h_o_r': Author of the package

     '_e_m_a_i_l': An email address to use in the Maintainer field

     '_u_r_l': URL

     '_b_i_o_c_V_i_e_w_s': Character data for the biocViews field of the
          DESCRIPTION file

_E_x_t_e_n_d_s:

     Class '"PDInfoPkgSeed"', directly. Class '"PkgSeed"', by class
     "PDInfoPkgSeed", distance 2.

_M_e_t_h_o_d_s:


     _c_h_i_p_N_a_m_e 'signature(object = "AffySNPCNVPDInfoPkgSeed")': ... 

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "AffySNPCNVPDInfoPkgSeed")': ... 

     _m_a_k_e_P_d_I_n_f_o_P_a_c_k_a_g_e 'signature(object = "AffySNPCNVPDInfoPkgSeed")':
          ... 

_N_o_t_e_s:

     The files used for slots 'splineParamFile', 'crlmmInfoFile', and
     'referenceDistFile' are generated by the Bioconductor project for
     each chip/platform and are hosted in our svn data repository at
     <URL:
     https://hedgehog.fhcrc.org/bioc-data/trunk/annotation/parms_store>.
     When 'makePdInfoPackage' is run, these files are simply copied to
     the 'inst/extdata' directory of the generated package.

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

     Benilton Carvalho

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

     showClass("AffySNPCNVPDInfoPkgSeed")

