cosmo-class              package:cosmo              R Documentation

_C_l_a_s_s "_c_o_s_m_o"

_D_e_s_c_r_i_p_t_i_o_n:

     An object of class '"cosmo"' is automatically created after
     calling the 'cosmo' function and summarizes the results.

_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("cosmo", ...)'.

_S_l_o_t_s:


     '_s_e_q_s': A list of the input sequences.

     '_p_w_m': An object of class 'pwm' representing the estimated
          position weight matrix.

     '_b_a_c_k': A data frame summarizing the candidate Markov models for
          the background distribution.

     '_t_m_a_t': The estimated transition matrix/matrices used to model the
          distribution of background nucleotides.

     '_c_a_n_d': A data frame summarizing the candidate models considered.

     '_c_o_n_s': The constraint set applied in the final model.

     '_s_e_l': The selected model.

     '_m_o_t_i_f_s': An object of class '"align"' representing the predicted
          motif occurrences.

     '_p_r_o_b_s': A list giving the posterior probabilities of motif
          occurrences along each sequence. 

     '_o_b_j_e_c_t_C_a_l_l': The call which produced this object. 

_M_e_t_h_o_d_s:


     _s_u_m_m_a_r_y 'signature(object = "cosmo",...)' Summarizes the cosmo
          object. 

     _p_l_o_t 'signature(x = "cosmo",type="PWM", ...)' If 'type == "PWM"',
          plots the sequence logo of the discovered motif. If 'type ==
          "prob"', plots the posterior probabilities of motif
          occurrences along all input sequences.


     _p_r_i_n_t 'signature(x = "cosmo",...)' Prints the discovered motifs
          along with the sequences they were discovered on, the
          starting positions, the strand, and the posterior probability
          of a motif occurrence at this site. Also prints the estimates
          position weight matrix.

     _s_h_o_w 'signature(object = "cosmo")' Prints the discovered motifs
          along with the sequences they were discovered on, the
          starting positions, the strand, and the posterior probability
          of a motif occurrence at this site. 

_A_u_t_h_o_r(_s):

     Oliver Bembom, bembom@berkeley.edu

