subMotifCon-class           package:cosmo           R Documentation

_C_l_a_s_s "_s_u_b_M_o_t_i_f_C_o_n" ~~~

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

     This class defines a global constraint when a part of the motif is
     partially known.

_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('subMotifCon','
      '    submotif      = ...., # Object of class \code{character}'
      '    minfreq       = ...., # Object of class \code{numeric}'
      '  )' or by: '  makeSubMotifCon('
      '    submotif      = ...., # Object of class \code{character}'
      '    minfreq       = ...., # Object of class \code{numeric}
     indicates the lower bound for the nucleotide frequencies in order
     for the submotif to be considered as contained within the
     motif.The nucleotide frequencies are determined from the
     estinmated position weight matrix.'
      '  )'

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


     '_s_u_b_m_o_t_i_f': Object of class '"matrix"', it is the submotif which
          is thought to be contained within the motif

     '_m_i_n_f_r_e_q': Object of class '"numeric"' indicates the lower bound
          for the nucleotide frequencies in order for the  submotif to
          be considered as contained within the motif. The nucleotide
          frequencies are determined from the estinmated position
          weight matrix.

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

     No methods defined with class "shapeDiffCon" in the signature.

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

     Fabian Gallusser, fgallusser@berkeley.edu

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

     'shapeCon', 'shapeDiffCon', 'posFreqCon', 'boundCon', 'palCon'
     'makeConSet'

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

     submotifcon=makeSubMotifCon("TATAA", 0.5)

