SnpSet                package:Biobase                R Documentation

_C_l_a_s_s _t_o _C_o_n_t_a_i_n _O_b_j_e_c_t_s _D_e_s_c_r_i_b_i_n_g _H_i_g_h-_T_h_r_o_u_g_h_p_u_t _S_N_P _A_s_s_a_y_s.

_D_e_s_c_r_i_p_t_i_o_n:

     Container for high-throughput assays and experimental metadata.
     'SnpSet' class is derived from 'eSet', and requires matricies
     'call', 'callProbability' as assay data members.

_E_x_t_e_n_d_s:

     Directly extends class 'eSet'.

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     'new('SnpSet', phenoData = [AnnotatedDataFrame], experimentData =
     [MIAME], annotation = [character], call = [matrix],
     callProbability = [matrix], ...) '

     'SnpSet' instances are usually created through 'new("SnpSet",
     ...)'. Usually the arguments to 'new' include 'call' (a matrix of
     gentoypic calls, with features (SNPs) corresponding to rows and
     samples to columns), 'phenoData', 'experimentData', and
     'annotation'.  'phenoData', 'experimentData', and 'annotation' can
     be missing, in which case they are assigned default values.

_S_l_o_t_s:

     Inherited from 'eSet':

     '_a_s_s_a_y_D_a_t_a': Contains matrices with equal dimensions, and with
          column number equal to 'nrow(phenoData)'. 'assayData' must
          contain a matrix 'call' with rows represening features (e.g.,
          SNPs) and columns representing samples, and a matrix
          'callProbability' describing the certainty of the call. The
          content of 'call' and 'callProbability' are not enforced by
          the class. Additional matrices of identical size may also be
          included in 'assayData'. Class:'AssayData-class' 

     '_p_h_e_n_o_D_a_t_a': See 'eSet'

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': See 'eSet'

     '_a_n_n_o_t_a_t_i_o_n': See 'eSet'

_M_e_t_h_o_d_s:

     Class-specific methods:

     '_e_x_p_r_s(_S_n_p_S_e_t)', '_e_x_p_r_s(_S_n_p_S_e_t,_m_a_t_r_i_x)<-' Access and set elements
          named 'call' in the 'AssayData' slot.

     Derived from 'eSet':

     '_u_p_d_a_t_e_O_b_j_e_c_t(_o_b_j_e_c_t, ..., _v_e_r_b_o_s_e=_F_A_L_S_E)' Update instance to
          current version, if necessary. See 'updateObject' and 'eSet'

     '_i_s_C_u_r_r_e_n_t(_o_b_j_e_c_t)' Determine whether version of object is
          current. See 'isCurrent'

     '_i_s_V_e_r_s_i_o_n_e_d(_o_b_j_e_c_t)' Determine whether object contains a
          'version' string describing its structure . See 'isVersioned'

     '_s_a_m_p_l_e_N_a_m_e_s(_S_n_p_S_e_t)' _a_n_d '_s_a_m_p_l_e_N_a_m_e_s(_S_n_p_S_e_t)<-': See 'eSet'

     '_f_e_a_t_u_r_e_N_a_m_e_s(_S_n_p_S_e_t)', '_f_e_a_t_u_r_e_N_a_m_e_s(_S_n_p_S_e_t, _v_a_l_u_e)<-': See
          'eSet'

     '_d_i_m_s(_S_n_p_S_e_t)': See 'eSet'

     '_p_h_e_n_o_D_a_t_a(_S_n_p_S_e_t)', '_p_h_e_n_o_D_a_t_a(_S_n_p_S_e_t,_v_a_l_u_e)<-': See 'eSet'

     '_v_a_r_L_a_b_e_l_s(_S_n_p_S_e_t)', '_v_a_r_L_a_b_e_l_s(_S_n_p_S_e_t, _v_a_l_u_e)<-': See 'eSet'

     '_v_a_r_M_e_t_a_d_a_t_a(_S_n_p_S_e_t)', '_v_a_r_M_e_t_a_d_a_t_a(_S_n_p_S_e_t,_v_a_l_u_e)<-': See 'eSet'

     '_p_D_a_t_a(_S_n_p_S_e_t)', '_p_D_a_t_a(_S_n_p_S_e_t,_v_a_l_u_e)<-': See 'eSet'

     '_v_a_r_M_e_t_a_d_a_t_a(_S_n_p_S_e_t)', '_v_a_r_M_e_t_a_d_a_t_a(_S_n_p_S_e_t,_v_a_l_u_e)' See 'eSet'

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a(_S_n_p_S_e_t)','_e_x_p_e_r_i_m_e_n_t_D_a_t_a(_S_n_p_S_e_t,_v_a_l_u_e)<-': See
          'eSet'

     '_p_u_b_M_e_d_I_d_s(_S_n_p_S_e_t)', '_p_u_b_M_e_d_I_d_s(_S_n_p_S_e_t,_v_a_l_u_e)' See 'eSet'

     '_a_b_s_t_r_a_c_t(_S_n_p_S_e_t)': See 'eSet'

     '_a_n_n_o_t_a_t_i_o_n(_S_n_p_S_e_t)', '_a_n_n_o_t_a_t_i_o_n(_S_n_p_S_e_t,_v_a_l_u_e)<-' See 'eSet'

     '_c_o_m_b_i_n_e(_S_n_p_S_e_t,_S_n_p_S_e_t)': See 'eSet'

     '_s_t_o_r_a_g_e_M_o_d_e(_e_S_e_t)', '_s_t_o_r_a_g_e_M_o_d_e(_e_S_e_t,_c_h_a_r_a_c_t_e_r)<-': See 'eSet'

     '_r_e_p_o_r_t_e_r_N_a_m_e_s(_S_n_p_S_e_t)', '_r_e_p_o_r_t_e_r_N_a_m_e_s(_S_n_p_S_e_t,_v_a_l_u_e)<-': DEPRECAT
          ED

     Standard generic methods:

     '_i_n_i_t_i_a_l_i_z_e(_S_n_p_S_e_t)': Object instantiation, used by 'new'; not to
          be called directly by the user.

     '_v_a_l_i_d_O_b_j_e_c_t(_S_n_p_S_e_t)': Validity-checking method, ensuring that
          'call' and 'callProbability' is a member of 'assayData'.
          'checkValidity(SnpSet)' imposes this validity check, and the
          validity checks of 'eSet'.

     '_s_h_o_w(_S_n_p_S_e_t)' See 'eSet'

     '_d_i_m(_S_n_p_S_e_t)', '_n_c_o_l' See 'eSet'

     '_S_n_p_S_e_t[(_i_n_d_e_x)': See 'eSet'

     '_S_n_p_S_e_t$', '_S_n_p_S_e_t$<-' See 'eSet'

_A_u_t_h_o_r(_s):

     V.J. Carey, after initial design by R. Gentleman

_S_e_e _A_l_s_o:

     'eSet', 'ExpressionSet'