uco                  package:seqinr                  R Documentation

_C_r_e_a_t_e _c_o_d_o_n _u_s_a_g_e _t_a_b_l_e

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

     'uco' calculates some codon usage index: the codon count 'eff',
     the absolute frequencies 'freq' or the Relative Synonymous Codon
     Usage 'rscu'.

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

     uco( seq, frame = 0, index = c("eff","freq","rscu"), as.data.frame = FALSE) 

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

     seq: a vector of chars 

   frame: an integer (0,1,2) giving the frame 

   index: One of this value 

as.data.frame: logical. If 'TRUE': The eff, freq and rscu index will be
          returned in a data frame.

_V_a_l_u_e:

     If 'as.data.frame' is TRUE 'uco' returns a data frame with five
     columns:  

     aa : a vector containing the name of amino-acid 

  codon : a vector containing the corresponding codon 

    eff : a numeric vector containing effectifs of codons 

   freq : a numeric vector containing frequencies of codons 

   rscu : a numeric vector containing the relative synonymous codon
          usage

    eff : a factor containing effectifs of codons 

   freq : a factor containing frequencies of codons 

   rscu : a factor containing the relative synonymous codon usage

_A_u_t_h_o_r(_s):

     D. Charif

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

      To have an overview of the seqinR's functionnality, please
     consult this vignette:  Charif, D., Lobry, J.R. (2005) SeqinR: a
     contributed package to the R project for statistical computing
     devoted to biological sequences retrieval and analysis. Springer
     Verlag, _Biological and Medical Physics/Biomedical Series_, in
     preparation. 

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

     s = read.fasta(File=system.file("sequences/malM.fasta",package = "seqinr"))
     uco( s[[1]], index="freq")
     uco( s[[1]], index="eff")
     uco( s[[1]], index="rscu")
     uco( s[[1]], as.data.frame = TRUE)

