chromLocation-class         package:annotate         R Documentation

_C_l_a_s_s _c_h_r_o_m_L_o_c_a_t_i_o_n, _a _c_l_a_s_s _f_o_r _d_e_s_c_r_i_b_i_n_g _g_e_n_e_s _a_n_d _t_h_e_i_r
_c_h_r_o_m_o_s_o_m_e _m_a_p_p_i_n_g_s.

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

     This class provides a mechanism for mapping a set of genes to
     their respective locations in chromosomes. Details on how to
     construct an object of this class from Bioconductor data packags
     are given in the 'byChroms' vignette in the 'geneplotter' package.

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     '  new('chromLocation','
      '    organism     = ...., # Object of class character'
      '    dataSource    = ...., # Object of class character'
      '    chromLocs    = ...., # Object of class list'
      '    probesToChrom  = ...., # Object of class environment'
      '    chromInfo    = ...., # Object of class numeric'
      '    geneSymbols  = ...., # Object of class environment'
      '  )'

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

     '_o_r_g_a_n_i_s_m': Object of class "character".  The organism that these
          genes correspond to. 

     '_d_a_t_a_S_o_u_r_c_e': Object of class "character".  The source of the gene
          data. 

     '_c_h_r_o_m_L_o_c_s': Object of class "list".  A list which provides
          specific location information for every gene. 

     '_p_r_o_b_e_s_T_o_C_h_r_o_m': Object of class "genEnv".  A hash table which
          will translate a probe identifier to chromosome it belongs
          to. 

     '_c_h_r_o_m_I_n_f_o': A numerical vector representing each chromosome,
          where the names are the names of the chromosomes and the
          values are their lengths

     '_g_e_n_e_S_y_m_b_o_l_s': An environment that maps a probe ID to the
          appropriate gene symbol

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

     _c_h_r_o_m_L_e_n_g_t_h_s (chromLocation): Gets the lengths of the chromosome
          for this organism

     _c_h_r_o_m_L_o_c_s (chromLocation): Gets the 'chromLocs' attribute. 

     _c_h_r_o_m_N_a_m_e_s (chromLocation): Gets the name of the chromosomes for
          this organism

     _d_a_t_a_S_o_u_r_c_e (chromLocation): Gets the 'dataSource' attribute. 

     _p_r_o_b_e_s_T_o_C_h_r_o_m (chromLocation): Gets the 'probesToChrom' attribute. 

     _n_C_h_r_o_m (chromLocation): gets the number of chromosomes this
          organism has

     _o_r_g_a_n_i_s_m (chromLocation): gets the 'organism' attribute. 

     _c_h_r_o_m_I_n_f_o Gets the 'chromInfo' attribute. 

     _g_e_n_e_S_y_m_b_o_l_s Gets the 'geneSymbols' attribute. 

