chkMotif4TF             package:harbChIP             R Documentation

_a_n_a_l_y_z_e _r_e_l_a_t_i_o_n_s_h_i_p _b_e_t_w_e_e_n _m_o_t_i_f _f_r_e_q_u_e_n_c_y
_a_n_d _b_i_n_d_i_n_g _i_n_t_e_n_s_i_t_y _f_o_r _s_e_l_e_c_t_e_d _m_o_t_i_f _a_n_d _T_F

_D_e_s_c_r_i_p_t_i_o_n:

     analyze relationship between motif frequency and binding intensity
     for selected motif and TF

_U_s_a_g_e:

     chkMotif4TF(motif, TF, chset, upstr, bthresh=2, countthresh=0)

_A_r_g_u_m_e_n_t_s:

   motif: character string in alphabet known to Biostrings

      TF: name of a TF (sample name in the ChIP-chip data structure
          'chset'

   chset: an ExpressionSet instance harboring ChIP-chip data 

   upstr: an instance of upstreamSeqs

 bthresh: threshold for binding intensity results to declare TF 'bound'
          to the upstream region

countthresh: threshold for motif count to be considered 'present' in
          upstream region

_D_e_t_a_i_l_s:

     Uses 'countPattern' to perform  motif count.

_V_a_l_u_e:

     a list with elements 'call', 'table', and 'test', the latter
     providing the result of 'fisher.test'

_A_u_t_h_o_r(_s):

     Vince Carey <stvjc@channing.harvard.edu>

_E_x_a_m_p_l_e_s:

     # slow
     ## Not run: 
     data(harbChIP)
     data(sceUpstr)
     chkMotif4TF("CGGCCG", "RDS1", harbChIP, sceUpstr)
     ## End(Not run)

