posFreqCon-class            package:cosmo            R Documentation

_C_l_a_s_s "_p_o_s_F_r_e_q_C_o_n" ~~~

_D_e_s_c_r_i_p_t_i_o_n:

     This class defines a constraint concerning the lower bound for the
     proportion of a nucleotide at a particular position of the
     interval

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form '  new('posFreqCon','
      '    pos       = ...., # Object of class character'
      '    nuc       = ...., # Object of class character'
      '    lower     = ...., # Object of class numeric'
      '  )' or by: '  makePosFreqCon('
      '    pos       = ...., # Object of class character'
      '    nuc       = ...., # Object of class character'
      '    lower     = ...., # Object of class numeric'
      '  )'

_S_l_o_t_s:

     '_p_o_s': Object of class '"numeric"' position in the interval of the
          nucleotide affected by the constraint 

     '_n_u_c': Object of class '"character"' nucleotide to which the
          constraint is applied  

     '_l_o_w_e_r': Object of class '"numeric"' lower bound for the
          nucleotide's frequency  

_M_e_t_h_o_d_s:

     No methods defined with class "posFreqCon" in the signature.

_N_o_t_e:

     ~~further notes~~

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

     Fabian Gallusser, fgallusser@berkeley.edu

_R_e_f_e_r_e_n_c_e_s:

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

     'boundCon', 'shapeCon', 'subMotifCon', 'shapeDiffCon', 'palCon'
     'makeConSet'

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

     set=makeConSet(2,c("B","V"),c(5,NA))
     posCon1=makePosFreqCon("2","A",0.5)
     posCon2=makePosFreqCon("All", "G", 0.3)
     conSet=addCon(set,list(posCon1,posCon2),c(1,2))
     # Because the first nucleotide position frequency constraint applies to
     #a specific position, it can only be applied to the interval of type "B".

