add_pseudo_counts           package:bgafun           R Documentation

_A_d_d _p_s_e_u_d_o _c_o_u_n_t_s _t_o _a_m_i_n_o _a_c_i_d _m_a_t_r_i_x _b_a_s_e_d _o_n _d_e_f_i_n_e_d _g_r_o_u_p_s

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

     This function will add pseudo counts to binary amino acid matrix
     based on the defined groups. It is used to minimise the effect of
     small sample size. The method of Henikoff and Henikoff is used to
     calculate the pseudocounts An alternative method is to simply add
     1 to the binary matrix

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

      add_pseudo_counts(amino,groups)

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

   amino: Matrix representation of alignment generated by
          convert_aln_amino 

  groups: Vector or factor that shows the group representation for each
          sequence in the alignment

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

     library(bgafun)
     data(LDH.amino.gapless)
     data(LDH.groups)
     LDH.pseudo=LDH.amino.gapless+1
     #or use the function 
     LDH.pseudo=add_pseudo_counts(LDH.amino.gapless,LDH.groups)

