cghExSet-class           package:Neve2006           R Documentation

_C_l_a_s_s "_c_g_h_E_x_S_e_t" _f_o_r _c_o_m_b_i_n_i_n_g _C_G_H _a_n_d _e_x_p_r_e_s_s_i_o_n _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     combination of an ExpressionSet and CGH assay results

_U_s_a_g_e:

     make_cghExSet(exprs, logRatios, cloneMeta, pd, mi, anno) # pd is AnnotatedDataFrame, mi is MIAME

_A_r_g_u_m_e_n_t_s:

   exprs: matrix of expression assay results 

logRatios: matrix of aCGH assay results 

cloneMeta: AnnotatedDataFrame for aCGH clone descriptions

      pd: AnnotatedDataFrame for sample level data 

      mi: 'MIAME' instance for experiment documentation 

    anno: character string with annotation platform descriptor for
          expression data

_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("cghExSet",
     phenoData, experimentData, annotation, exprs, logRatios,
     cloneMeta)'.

_S_l_o_t_s:

     '_c_g_h_A_s_s_a_y_s': Object of class '"AssayData"' rectangular
          representation of logRatio data from CGH 

     '_c_l_o_n_e_M_e_t_a': Object of class '"AnnotatedDataFrame"' information on
          chromosome and offset of clones

     '_a_s_s_a_y_D_a_t_a': Object of class '"AssayData"' expression assay
          results 

     '_p_h_e_n_o_D_a_t_a': Object of class '"AnnotatedDataFrame"' sample level
          data 

     '_f_e_a_t_u_r_e_D_a_t_a': Object of class '"AnnotatedDataFrame"' reporter
          level metadata for expression assay results 

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': Object of class '"MIAME"' container for
          experiment documentation 

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"character"' identifiers for
          expression and CGH platforms, as a named vector with elements
          named 'exprs' and 'logRatios' 

     '.___c_l_a_s_s_V_e_r_s_i_o_n__': Object of class '"Versions"'  

_E_x_t_e_n_d_s:

     Class 'eSet-class', directly. Class 'VersionedBiobase-class', by
     class "eSet", distance 2. Class 'Versioned-class', by class
     "eSet", distance 3.

_M_e_t_h_o_d_s:

     _c_l_o_n_e_M_e_t_a 'signature(cghSet = "cghExSet")': extract annotated data
          frame on clone locations for CGH component 

     _c_l_o_n_e_N_a_m_e_s 'signature(cghSet = "cghExSet")': extract character
          vector of clone IDs for CGH component 

     _e_x_p_r_s 'signature(object = "cghExSet")': extract expression assay
          results 

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "cghExSet")': infrastructure 

     _l_o_g_R_a_t_i_o_s 'signature(cghSet = "cghExSet")': extract CGH assay
          results 

     _s_h_o_w 'signature(object = "cghExSet")': display object in concise
          form 

_A_u_t_h_o_r(_s):

     V Carey <stvjc@channing.harvard.edu>

_R_e_f_e_r_e_n_c_e_s:

     R. M. Neve Cancer Cell Dec 2006

_E_x_a_m_p_l_e_s:

     showClass("cghExSet")
     data(neveExCGH)
     logRatios(neveExCGH)[1:4,]
     exprs(neveExCGH)[1:4,]

