postProbs-class            package:cosmo            R Documentation

_C_l_a_s_s "_p_o_s_t_P_r_o_b_s"

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

     An object of class '"postProbs"' collects information about the
     posterior probability of motif occurrences in each of the eligible
     positions of the input sequences. Most notably these probabilities
     can be plotted using the plot function.

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

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

     '_s_e_q_M_a_t': Object of class '"matrix"' The sequences in numerical
          matrix format as output by cosmo.

     '_s_e_q_N_a_m_e_s': '"list"'A list of the sequence names.

     '_p_r_o_b_s': '"numeric"'A matrix of the posterior probabilities.

     '_r_e_v_c_o_m_p': '"logical"'A matrix indicating whether the motif is
          more likely to occure in the reverse complement orientation. 

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

_p_l_o_t 'signature(x = "postProbs")' Plots the posterior probabilities. If
     the motif is more likely to occur in the forward strand
     orientation, the bar extends upward from the horizontal, otherwise
     it extends downward.

_N_o_t_e:

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

     Oliver Bembom, bembom@berkeley.edu

_R_e_f_e_r_e_n_c_e_s:

_S_e_e _A_l_s_o:

_E_x_a_m_p_l_e_s:

