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 chromosomal information provided by a
     Bioconductor metadata package.  By creating the object once for a
     particular package, it can be used in a variety of locations
     without the need to recomputed values repeatedly.

_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. 

_S_e_e _A_l_s_o:

     'buildChromLocation'

_E_x_a_m_p_l_e_s:

        curWarn <- getOption("warn")
        options(warn=0)
        on.exit(options(warn=curWarn), add=TRUE)
        if (require("hgu95av2")) {
          z <- buildChromLocation("hgu95av2")

          ## find the number of chromosomes
          nChrom(z)

          ## Find the names of the chromosomes
          chromNames(z)

          ## get the organism this object refers to
          organism(z)

          ## get the lengths of the chromosomes in this object
          chromLengths(z)

        } else print("This example requires the hgu95av2 data package")