makeShapeDiffCon            package:cosmo            R Documentation

_C_o_n_s_t_r_u_c_t_i_n_g _a _s_h_a_p_e _p_a_r_a_m_e_t_e_r _d_i_f_f_e_r_e_n_c_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 'shapeDiffCon' object representing a
     constraint on the unknown position weight matrix that requires the
     the difference between the information content at the edge of one
     interval and the information content at the edge of another
     interval to be bounded betwene given bounds. This constraint may
     only be applied to intervals that already have a shape constraint.

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

     makeShapeDiffCon(int1, int2, lower, upper)

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

    int1: 'character' the location of the first information content of
          interest. This is specified as the number of the interval
          followed by the letter 'a' or 'b' depending on whether the
          left or right edge of the interval is desired.

    int2: 'character' the location of the second information content of
          interest. This is specified as the number of the interval
          followed by the letter 'a' or 'b' depending on whether the
          left or right edge of the interval is desired.

   lower: 'numeric' the lower bound on the difference in information
          contents.

   upper: 'numeric' the upper bound on the difference in information
          contents.

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

     An object of class 'shapeDiffCon'.

_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:

     ## continuous information content across interval 1
     sdc1 <- makeShapeDiffCon("1a", "1b", 0.0, 0.0)

     ## continuous information content at junction
     ## between intervals 1 and 2
     sdc2 <- makeShapeDiffCon("1b", "2a", 0.0, 0.0)

     ## decreasing information content across interval 1
     sdc3 <- makeShapeDiffCon("1a", "1b", 0.0, 2.0)

