align-class              package:cosmo              R Documentation

_C_l_a_s_s "_a_l_i_g_n"

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

     An object of class '"align"' summarizes the motif occurrences that
     were predicted by 'cosmo'. For each predicted motif occurrence, it
     contains the sequences on which the site was found, the position
     on that sequence, the orientation of the motif (1 if found on the
     forward strand, -1 otherwise), the site itself, as well as the
     posterior probability of a motif occurrence at that site.

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

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


     '_s_e_q': Object of class '"numeric"' The sequences on which the
          sites were predicted.

     '_p_o_s': Object of class '"numeric"' The starting postions of the
          discovered sites. 

     '_o_r_i_e_n_t': Object of class '"numeric"' The orientation in which
          each motif was discovered: 1 for the forward strand
          orientation, and -1 for the reverse complement orientation

     '_m_o_t_i_f': Object of class '"character"' The site that was predicted
          to be a motif occurrence. 

     '_p_r_o_b': Object of class '"numeric"' The posterior probability of a
          motif occurrence at this position 

     '_e_v_a_l': Object of class '"numeric"' The E-value of the multiple
          alignment containing the predicted motif occurrences 

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


     _s_u_m_m_a_r_y 'signature(object = "align",...)' 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 E-value
          of the discovered alignment.

     _p_r_i_n_t 'signature(x = "align",...)' 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. 

     _s_h_o_w 'signature(object = "align")' 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

