SMAPObservations-class         package:SMAP         R Documentation

_C_l_a_s_s "_S_M_A_P_O_b_s_e_r_v_a_t_i_o_n_s": _A _c_l_a_s_s _t_o _m_a_n_a_g_e _m_i_c_r_o_a_r_r_a_y
_o_b_s_e_r_v_a_t_i_o_n_s _f_o_r _t_h_e _S_M_A_P _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     Holds observed microarray intensity ratios and clone annotations
     for the 'SMAP' package.

_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("SMAPObservations", value, chromosome, startPosition,
     endPosition, name, reporterId)'.  You can also use the convenience
     function 'SMAPObservations'.

_S_l_o_t_s:


     '_v_a_l_u_e': Object of class '"numeric"' Microarray intensity ratios.

     '_c_h_r_o_m_o_s_o_m_e': Object of class '"character"' Associated chromosomes
          for the observations.

     '_s_t_a_r_t_P_o_s_i_t_i_o_n': Object of class '"numeric"' Associated start
          positions for the observations.

     '_e_n_d_P_o_s_i_t_i_o_n': Object of class '"numeric"' Associated end
          positions for the observations.

     '_r_e_p_o_r_t_e_r_I_d': Object of class '"character"' Identifiers of the
          observations, e.g., probe ids.

     '_n_a_m_e': Object of class '"character"' An identifier of the
          observation set.

     '_n_o_O_b_s_e_r_v_a_t_i_o_n_s': Object of class '"numeric"' The number of
          observations in the set.

_M_e_t_h_o_d_s:


     _v_a_l_u_e 'signature(object = "SMAPObservations")': Returns the values
          of the observations.

     _c_h_r_o_m_o_s_o_m_e 'signature(object = "SMAPObservations")': Returns the
          chromosome annotations of the observations.

     _s_t_a_r_t_P_o_s_i_t_i_o_n 'signature(object = "SMAPObservations")': Returns
          the start positions of the observations.

     _e_n_d_P_o_s_i_t_i_o_n 'signature(object = "SMAPObservations")': Returns the
          end positions of the observations.

     _r_e_p_o_r_t_e_r_I_d 'signature(object = "SMAPObservations")': Returns the
          identifiers of the observations.

     _n_a_m_e 'signature(object = "SMAPObservations")': Returns the name of
          the observation set.

     _n_o_O_b_s_e_r_v_a_t_i_o_n_s 'signature(object = "SMAPObservations")': Returns
          the number of observations in the set.

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "SMAPObservations")': Creates an
          instance.

     _p_l_o_t 'signature(x = "SMAPObservations", y = "missing")': A plot
          method for the observations.

     [ 'signature(x = "SMAPPObservations")': Creates a new object of
          class SMAPObservations with extracted elements as specified
          by the indices provided.

_A_u_t_h_o_r(_s):

     Robin Andersson, robin.andersson@lcb.uu.se

_R_e_f_e_r_e_n_c_e_s:

     Andersson, R., Bruder, C. E. G., Piotrowski, A., Menzel, U., Nord,
     H., Sandgren, J., Hvidsten, T. R., Diaz de Stahl, T., Dumanski, J.
     P., Komorowski, J., A Segmental Maximum A Posteriori Approach to
     Array-CGH Copy Number Profiling, submitted

_S_e_e _A_l_s_o:

     'smap', 'SMAPObservations'

