chkMotif4TF             package:harbChIP             R Documentation

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_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)

