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 ANY'
      '    chromInfo    = ...., # Object of class numeric'
      '    geneSymbols  = ...., # Object of class ANY'
      '  )'

_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': An object with an environment-like API 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 or an object with environment-like
          API 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:

       library("hgu95av2.db")

       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)

