AffySNPPDInfoPkgSeed-class   package:pdInfoBuilder   R Documentation

_C_l_a_s_s "_A_f_f_y_S_N_P_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
     mapping (SNP chip) 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("AffySNPPDInfoPkgSeed", splineParamFile, crlmmInfoFile,
     referenceDistFile, ...)'.

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


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

     '_c_r_l_m_m_I_n_f_o_F_i_l_e': 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': Reference distribution file used in the
          normalization step by 'snprma'.

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

     '_c_s_v_A_n_n_o_F_i_l_e': Affymetrix CSV Annotation file.

     '_c_s_v_S_e_q_F_i_l_e': Affymetrix Probe Sequence file.

     '_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

     '_u_r_l': chip URL

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

     '_o_r_g_a_n_i_s_m': organism for chip. 

     '_s_p_e_c_i_e_s': species for chip.   

     '_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

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

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


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

     _g_e_t_G_e_o_m_e_t_r_y 'signature(object = "AffySNPPDInfoPkgSeed")': ... 

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

_N_o_t_e:

     *IMPORTANT* The user is strongly advised to download Affymetrix
     SNP packages from BioConductor.

     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.

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

     showClass("AffySNPPDInfoPkgSeed")

     cdfFile <- "Mapping250K_Nsp.cdf"
     csvAnno <- "Mapping250K_Nsp_annot.csv"
     csvSeq <- "Mapping250K_Nsp_probe_tab"

     spline <- "pd.mapping250k.nsp.spline.params.rda"
     refd <- "pd.mapping250k.nspRef.rda"
     crlmmInf <- "pd.mapping250k.nspCrlmmInfo.rda"

     pkg <- new("AffySNPPDInfoPkgSeed", 
                version="0.1.5",
                author="A. U. Thor", email="au@thor.net",
                biocViews="AnnotationData",
                genomebuild="NCBI Build 35, May 2004",
                cdfFile=cdfFile, csvAnnoFile=csvAnno, csvSeqFile=csvSeq,
                splineParamFile=spline, crlmmInfoFile=crlmmInf,
                referenceDistFile=refd)

     showMethods(classes=class(pkg))

