makeSubMotifCon            package:cosmo            R Documentation

_C_o_n_s_t_r_u_c_t_i_n_g _a _s_u_b_m_o_t_i_f _c_o_n_s_t_r_a_i_n_t

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

     This function constructs a \texttt{subMotifCon} object
     representing a constraint on the unknown position weight matrix
     that requires the motif to contain a given submotif

_U_s_a_g_e:

     makeSubMotifCon(submotif, minfreq)

_A_r_g_u_m_e_n_t_s:

submotif: 'character' the submotif

 minfreq: 'numeric' roughly, the minimum frequency with which
          nucleotides in the submotif must occur in the motif

_D_e_t_a_i_l_s:

_V_a_l_u_e:

     An object of class \texttt{subMotifCon}.

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

     Fabian Gallusser, fgallusser@berkeley.edu

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

     'boundCon', 'shapeCon', 'subMotifCon', 'posFreqCon',
     'shapeDiffCon', 'palCon'

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

     pfc <- makeSubMotifCon("CGC", 0.8)

