fuzzygenet               package:ade4               R Documentation

_R_e_a_d_i_n_g _a _t_a_b_l_e _o_f _g_e_n_e_t_i_c _d_a_t_a (_d_i_p_l_o_i_d _i_n_d_i_v_i_d_u_a_l_s)

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

     Reads data like 'char2genet' without a priori population

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

     fuzzygenet(X)

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

       X: a data frame of strings of characters (individuals in row,
          locus in variables), the value coded '000000' or two alleles
          of 6 characters 

_D_e_t_a_i_l_s:

     In entry, a row is an individual, a variable is a locus and a
     value is a string of characters, for example,  012028 for a
     heterozygote carying alleles 012 and 028; 020020 for a homozygote
     carrying two alleles 020 and 000000 for a not classified locus
     (missing data).

     In exit, a fuzzy array with the following encoding for a locus:
      0 0   1   ...   0 for a homozygote 
      0 0.5 0.5 ...   0 for a heterozygote 
      p1    p2  p3  ...   pm for an unknown where (p1 p2  p3  ...   pm)
     is the observed allelic frequencies for all tha available data.

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

     returns a data frame with the 6 following attributs: 

col.blocks : a vector containing the number of alleles by locus

all.names : a vector containing the names of alleles

loc.names : a vector containing the names of locus

  row.w : a vector containing the uniform weighting of rows

col.freq : a vector containing the global allelic frequencies

col.num : a factor ranking the alleles by locus

_N_o_t_e:

     In the exit data frame, the alleles are numbered 1, 2, 3, ... by
     locus and the loci are called L01, L02, L03, ... for the
     simplification of listing. The original names are kept.

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

     Daniel Chessel chessel@biomserv.univ-lyon1.fr

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

     ~put references to the literature/web site here ~

_S_e_e _A_l_s_o:

     'char2genet' if you have the a priori definition of the groups of
     individuals (populations). It may be used on the created object
     'dudi.fca'

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

     data(casitas)
     casitas[1:5, ]
     casitas <- fuzzygenet(casitas)
     attributes(casitas)
     rm(casitas)

