alphabetFrequency         package:Biostrings         R Documentation

_F_u_n_c_t_i_o_n _t_o _c_a_l_c_u_l_a_t_e _t_h_e _f_r_e_q_u_e_n_c_y _o_f _l_e_t_t_e_r_s _i_n _a _b_i_o_l_o_g_i_c_a_l _s_e_q_u_e_n_c_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function calculates the frequency of each letter in the
     (base) alphabet for a biological sequence.

_U_s_a_g_e:

       alphabetFrequency(x, baseOnly=TRUE)

_A_r_g_u_m_e_n_t_s:

       x: A BString, DNAString, RNAString or BStringViews object. 

baseOnly: 'TRUE' or 'FALSE'. If 'TRUE', the returned vector only
          contains frequencies for the letters in the "base" alphabet +
          the gap symbol i.e. "A", "C", "G", "T" + "-" when 'x' is a
          DNAString object (or a BStringViews object with a DNAString
          subject), and "U", "G", "C", "A" + "-" when 'x' is a
          RNAString object (or a BStringViews object with a RNAString
          subject). When 'x' is a BString object (or a BStringViews
          object with a BString subject), then the 'baseOnly' argument
          is ignored. 

_V_a_l_u_e:

     An integer vector. If 'x' is a DNAString or RNAString object (or a
     BStringViews object with a DNAString or RNAString subject), then
     the returned vector is named with the letters in the alphabet. If
     the 'baseOnly' argument is TRUE, then the returned vector has an
     extra element named 'other'. If 'x' is a BStringViews object, then
     the returned vector contains the cumulated frequencies found in
     each view.

_A_u_t_h_o_r(_s):

     H. Pages

_S_e_e _A_l_s_o:

     BString, DNAString, RNAString, BStringViews

_E_x_a_m_p_l_e_s:

       data(yeastSEQCHR1)
       yeast1 <- DNAString(yeastSEQCHR1)
       alphabetFrequency(yeast1)
       alphabetFrequency(yeast1, baseOnly=FALSE)