Calculate_Row_Weights         package:bgafun         R Documentation

_C_a_l_c_u_l_a_t_e _t_h_e _s_e_q_u_e_n_c_e _w_e_i_g_h_t_s _f_o_r _a_l_l _t_h_e _r_o_w_s _i_n _m_y _a_m_i_n_o,_u_s_i_n_g _l_a_b_e_l _a_s _t_h_e _g_r_o_u_p_i_n_g

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

     This will calculate the sequence weights for each group using the
     Heinkoff and Heinkoff method.  Each residue in the sequence is
     assigned a weight depending on how unique it is in the column. The
     sequence weight is then the sum of these weights, and the total
     weight is the number of groups

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

      Calculate_Row_Weights(my_amino,label)

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

my_amino: Matrix representation of alignment generated by
          convert_aln_amino 

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

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

     Henikoff, S. and J. G. Henikoff (1994). "Position-based sequence
     weights." J Mol Biol 243(4): 574-8.

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

     library("bgafun")
     data(LDH.amino.gapless)
     data(LDH.groups)
     LDH.weights=Calculate_Row_Weights(LDH.amino.gapless,LDH.groups)
     sum(LDH.weights)

