makeShapeCon              package:cosmo              R Documentation

_C_o_n_s_t_r_u_c_t_i_n_g _a _s_h_a_p_e _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 'shapeCon' object representing a
     constraint on the unknown position weight matrix that requires the
     information content to follow a particular functional form.

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

     makeShapeCon(shape, sLower, sUpper, eLower, eUpper, error)

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

   shape: 'character' the functional form of the information content.
          This must be either 'Linear', 'MonotoneIncreasing', or
          'MonotoneDecreasing'.

  sLower: 'numeric' lower bound on the information content at the start
          of the interval

  sUpper: 'numeric' upper bound on the information content at the start
          of the interval

  eLower: 'numeric' lower bound on the information content at the end
          of the interval

  eUpper: 'numeric' upper bound on the information content at the end
          of the interval

   error: 'numeric' tolerance for how much the actual information
          content profile is allowed to deviate from the prescribed
          form

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

     An object of class 'shapeCon'.

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

     Fabian Gallusser, fgallusser@berkeley.edu

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

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

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

     sc <- makeShapeCon("Linear",1.0, 2.0, 1.5, 2.0, 0.05)

