convert_aln_AAP            package:bgafun            R Documentation

_C_o_n_v_e_r_t_s _a_l_i_g_n_m_e_n_t _i_n_t_o _a _m_a_t_r_i_x _u_s_i_n_g _t_h_e _a_m_i_n_o _a_c_i_d _p_r_o_p_e_r_t_y _e_n_c_o_d_i_n_g

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

     Each residue in the alignment is represented by a vector of five
     continuous variables as given by Atchley et al  They applied a
     multivariate statistic approach to reduce the information in 494
     amino acid attributes into a set of five factors for each amino
     acid.  Factor A is termed the polarity index. It correlates well
     with a large variety of descriptors including the number of
     hydrogen bond donors, polarity versus nonpolarity, and
     hydrophobicity versus hydrophilicity.  Factor B is a secondary
     structure index. It represents the propensity of an amino acid to
     be in a particular type of secondary structure, such as a coil,
     turn or bend versus the frequency of it in an a-helix.  Factor C
     is correlated with molecular size, volume and molecular weight. 
     Factor D reflects the number of codons coding for an amino acid
     and amino acid composition. These attributes are related to
     various physical properties including refractivity and heat
     capacity.  Factor E is related to the electrostatic charge.  Gaps
     are represented by five zeros and should be either removed or
     replaced by the average of the column for a particular group.

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

      convert_aln_AAP(Alignment)

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

Alignment: Alignment object read in using read.alignment function in
          seqinr 

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

     Atchley, W. R., J. Zhao, et al. (2005). "Solving the protein
     sequence metric problem." Proc Natl Acad Sci U S A 102(18):
     6395-400.

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

     library(bgafun)
     data(LDH)
     data(LDH.groups)
     LDH.aap=convert_aln_AAP(LDH)
     dim(LDH.aap)
     LDH.aap.ave=average_cols_aap(LDH.aap,LDH.groups)
     dim(LDH.aap.ave)

