create_profile_strings        package:bgafun        R Documentation

_C_r_e_a_t_e _a _p_r_o_f_i_l_e _s_t_r_i_n_g _f_o_r _e_a_c_h _g_r_o_u_p _i_n _a_n _a_l_i_g_n_m_e_n_t

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

     This function is used to analysis the amino acids at each position
     in the alignment. It can be used to analysis the columns that the
     bga analysis identified as interesting It creates a profile
     string, 1D vector which shows the number of amino acids at each
     position in an alignment for each group that has been defined

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

      create_profile_strings(x,y)

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

       x: Matrix representation of alignment generated by
          convert_aln_amino 

       y: 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.groups)
     data(LDH.amino.gapless)
     #run the analysis
     LDH.binary.bga=bga(t(LDH.amino.gapless+1),LDH.groups)
     #Get the important residues
     top_res=top_residues_2_groups(LDH.binary.bga)
     #To tidy up the results
     names(top_res)=sub("X","",names(top_res))
     # and now look at the amino acid content in the alignment 
     LDH.profiles=create_profile_strings(LDH.amino.gapless,LDH.groups)
     # and now look at only those columns that are identified by BGA
     #LDH.profiles[,(colnames(LDH.profiles) 

