makePosFreqCon             package:cosmo             R Documentation

_C_o_n_s_t_r_u_c_t_i_n_g _a _n_u_c_l_e_o_t_i_d_e _f_r_e_q_u_e_n_c_y _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{posFreqCon} object representing
     a constraint on the unknown position weight matrix that requires
     the frequency of a given nucleotide to be above a given lower
     bound, either at a single position in a given interval, or on
     average across the entire interval

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

     makePosFreqCon(pos, nuc, lower)

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

     pos: This is either the string 'avg', indicating that the average
          nucleotide frequency across the interval is bounded from
          below, or a position in the interval, indicating the
          nucleotide frequency at that position in the interval is
          bounded from below.

     nuc: 'character' This is one of 'A', 'C', 'G', 'T', 'GC', 'AT'.

   lower: 'numeric' the lower bound on the nucleotide frequency of
          interest

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

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

     An object of class \texttt{posFreqCon}.

_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 <- makePosFreqCon("avg","GC", 0.75)

