geneSet-class          package:GeneticsBase          R Documentation

_C_l_a_s_s "_g_e_n_e_S_e_t", _a _c_l_a_s_s _f_o_r _g_e_n_e_t_i_c_s _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     A fundamental data structure for genetic 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("geneSet", ...)'.
     ~~ describe objects here ~~

_S_l_o_t_s:


     '_c_a_l_l_C_o_d_e_s': matrix of positive integers,  giving genotype calls. 
          Each row is a locus (marker);  each column is an individual
          (sample).  Each element  is a row index into a matrix in the
          list of translation  tables stored in the transTables slot. 
          Must have row  and column names.

     '_e_r_r_o_r_M_e_t_r_i_c_s': numeric matrix, parallel to the  callCodes matrix.
           Each element gives an uncertainty measure  for the
          corresponding element of the callCodes matrix.  Must  have
          row and column names.

     '_t_r_a_n_s_T_a_b_l_e_s': list of code translation tables.  The  list must
          have names.  Each component is a matrix, and must  include a
          column named "levels".

     '_m_i_s_s_i_n_g_C_o_d_e_s': list of allele missing-value codes,  parallel to
          the transTables list.  The list must have the same  names as
          the list in the transTables slot.  Each component is  a
          character vector.  Any allele symbol in component "abc" of 
          the transTables list that appears in component "abc" of the 
          missingCodes list is to be interpreted as a missing value by 
          functions operating on the geneSet object. An empty list will
          be  interpreted to mean that the data contains no missing
          values.

     '_s_a_m_p_l_e_I_n_f_o': Object of class '"data.frame"' 

     '_m_a_r_k_e_r_I_n_f_o': a dataframe, with one row for each row  in the
          callCodes matrix.  Must include columns "Name" and 
          "TransTable".  

     '_s_t_u_d_y_I_n_f_o': Object of class '"list"' ~~ 

     '_d_e_s_c_r_i_p_t_i_o_n': Object of class '"character"' ~~ 

     '_n_o_t_e_s': Object of class '"character"' ~~ 

     '_p_l_o_i_d_y': Object of class '"numeric"' ~~ 

     '_p_h_a_s_e': 1. Yes/No for all (logical scalar) 2. Yes/No for each
          Marker (logical vector) 3. phaseObject (TBD): observation by
          marker by phase probabilities + definitions of contigs +
          probability of contigs 


_M_e_t_h_o_d_s:


     _H_W_E 'signature(object = "geneSet")': Hardy-Weinberg Equilibrium
          Significance Test 

     _L_D 'signature(object = "geneSet")': ... 

     _L_D_b_a_n_d 'signature(object = "geneSet")': ... 

     _L_D_d_i_s_t 'signature(object = "geneSet")': ... 

     [ 'signature(x = "geneSet")': ... 

     [[ 'signature(x = "geneSet")': ... 

     _a_l_l_e_l_e_C_o_u_n_t 'signature(object = "geneSet")': ... 

     _a_l_l_e_l_e_L_e_v_e_l_s 'signature(object = "geneSet")': ... 

     _a_l_l_e_l_e_s 'signature(object = "geneSet")': ... 

     _c_a_l_l_C_o_d_e_s 'signature(object = "geneSet")': ... 

     _c_a_l_l_C_o_d_e_s<- 'signature(object = "geneSet")': ... 

     _c_a_r_r_i_e_r 'signature(object = "geneSet")': ... 

     _d_e_s_c_r_i_p_t_i_o_n 'signature(object = "geneSet")': ... 

     _d_e_s_c_r_i_p_t_i_o_n<- 'signature(object = "geneSet")': ... 

     _d_o_m_i_n_a_n_t 'signature(object = "geneSet")': ... 

     _e_r_r_o_r_M_e_t_r_i_c_s 'signature(object = "geneSet")': ... 

     _e_r_r_o_r_M_e_t_r_i_c_s<- 'signature(object = "geneSet")': ... 

     _g_e_n_o_t_y_p_e_L_e_v_e_l_s 'signature(object = "geneSet")': ... 

     _g_e_n_o_t_y_p_e_s 'signature(object = "geneSet")': ... 

     _h_e_a_d 'signature(x = "geneSet")': ... 

     _h_e_t_e_r_o_z_y_g_o_t_e 'signature(object = "geneSet")': ... 

     _h_o_m_o_z_y_g_o_t_e 'signature(object = "geneSet")': ... 

     _m_a_r_k_e_r_I_n_f_o 'signature(object = "geneSet")': ... 

     _m_a_r_k_e_r_I_n_f_o<- 'signature(object = "geneSet")': ... 

     _m_a_r_k_e_r_N_a_m_e_s 'signature(object = "geneSet")': ... 

     _m_i_s_s_i_n_g_C_o_d_e_s 'signature(object = "geneSet")': ... 

     _m_i_s_s_i_n_g_C_o_d_e_s<- 'signature(object = "geneSet")': ... 

     _n_a_l_l_e_l_e 'signature(object = "geneSet")': ... 

     _n_m_a_r_k_e_r 'signature(object = "geneSet")': ... 

     _n_o_b_s 'signature(x = "geneSet")': ... 

     _n_o_t_e_s 'signature(object = "geneSet")': ... 

     _n_o_t_e_s<- 'signature(object = "geneSet")': ... 

     _p_h_a_s_e 'signature(object = "geneSet")': ... 

     _p_h_a_s_e<- 'signature(object = "geneSet")': ... 

     _p_l_o_i_d_y 'signature(object = "geneSet")': ... 

     _p_l_o_i_d_y<- 'signature(object = "geneSet")': ... 

     _r_e_c_e_s_s_i_v_e 'signature(object = "geneSet")': ... 

     _s_a_m_p_l_e_I_n_f_o 'signature(object = "geneSet")': ... 

     _s_a_m_p_l_e_I_n_f_o<- 'signature(object = "geneSet")': ... 

     _s_h_o_w 'signature(object = "geneSet")': ... 

     _s_t_u_d_y_I_n_f_o 'signature(object = "geneSet")': ... 

     _s_t_u_d_y_I_n_f_o<- 'signature(object = "geneSet")': ... 

     _t_a_i_l 'signature(x = "geneSet")': ... 

     _t_r_a_n_s_T_a_b_l_e_s 'signature(object = "geneSet")': ... 

     _t_r_a_n_s_T_a_b_l_e_s<- 'signature(object = "geneSet")': ... 

_N_o_t_e:

     ~~further notes~~

_A_u_t_h_o_r(_s):

     J.Cheng, modified by S. Chasalow, and Gregory R. Warnes
     <warnes@bst.rochester.edu>

_R_e_f_e_r_e_n_c_e_s:

     ~put references to the literature/web site here ~

_E_x_a_m_p_l_e_s:

     ##---- Should be DIRECTLY executable !! ----

