racExSet-class            package:GGBase            R Documentation

_C_l_a_s_s "_r_a_c_E_x_S_e_t" - _c_o_n_t_a_i_n_e_r _f_o_r _g_e_n_o_t_y_p_e _d_a_t_a
_i_n '_r_a_r_e _a_l_l_e_l_e _c_o_u_n_t' _f_o_r_m _a_n_d _e_x_p_r_e_s_s_i_o_n _d_a_t_a.  _A_p_p_r_o_a_c_h_i_n_g
_o_b_s_o_l_e_s_c_e_n_c_e, _s_e_e _s_m_l_S_e_t _f_o_r _m_o_r_e _e_f_f_i_c_i_e_n_t _r_e_p_r_e_s_e_n_t_a_t_i_o_n.

_D_e_s_c_r_i_p_t_i_o_n:

     Class "racExSet" - container for genotype data in 'rare allele
     count' form and expression data.  Approaching obsolescence, see
     smlSet for more efficient representation.

_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("racExSet",
     phenoData, experimentData, annotation, exprs, racs, rarebase,
     SNPalleles)'.

_S_l_o_t_s:


     '_r_a_c_A_s_s_a_y_s': Object of class '"AssayData"' S x N matrix holding
          rare allele counts 

     '_r_a_r_e_b_a_s_e': Object of class '"character"' nucleotide code for rare
          allele of each SNP in the population assayed 

     '_S_N_P_a_l_l_e_l_e_s': Object of class '"character"'  nucleotide code for
          polymorphism 

     '_a_s_s_a_y_D_a_t_a': Object of class '"AssayData"' expression data
          container 

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

     '_f_e_a_t_u_r_e_D_a_t_a': Object of class '"AnnotatedDataFrame"' expression
          feature metadata container 

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': Object of class '"MIAME"' experiment level
          metadata 

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"character"' Bioconductor
          annotation package name 

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

_E_x_t_e_n_d_s:

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

_M_e_t_h_o_d_s:


     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "racExSet")': ... 

_A_u_t_h_o_r(_s):

     VJ Carey <stvjc@channing.harvard.edu>

_S_e_e _A_l_s_o:

     murine examples in GGtools continue to use this structure

_E_x_a_m_p_l_e_s:

     showClass("racExSet")

