import            package:adegenet            R Documentation(utf8)

_I_m_p_o_r_t_i_n_g _d_a_t_a _f_r_o_m _s_e_v_e_r_a_l _s_o_f_t_w_a_r_e_s _t_o _a _g_e_n_i_n_d _o_b_j_e_c_t

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

     Their are several ways to import genotype data to a genind object:
     i) from a data.frame with a given format (see 'df2genind'), ii)
     from a file with a recognized extension, or iii) from an
     alignement of sequences (see 'DNAbin2genind').

     The function 'import2genind' detects the extension of the file
     given in argument and seeks for an appropriate import function to
     create a 'genind' object.
      Current recognized formats are :
      - GENETIX files (.gtx) 
      - Genepop files (.gen) 
      - Fstat files (.dat) 
      - STRUCTURE files (.str or .stru) 

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

     import2genind(file,missing=NA,quiet=FALSE, ...)

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

    file: a character string giving the path to the file to convert,
          with the appropriate extension.

 missing: can be NA, 0 or "mean". See details section.

   quiet: logical stating whether a conversion message must be printed
          (TRUE,default) or not (FALSE).

     ...: other arguments passed to the appropriate 'read' function
          (currently passed to 'read.structure')

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

     There are 3 treatments for missing values: 
      - NA: kept as NA.

     - 0: allelic frequencies are set to 0  on all alleles of the
     concerned locus. Recommended for a PCA on compositionnal data.

     - "mean": missing values are replaced by the mean frequency of the
     corresponding allele, computed on the whole set of individuals.
     Recommended for a centred PCA.

     Beware: same data in different formats are not expected to produce
      exactly the same 'genind' objects.
      For instance, conversions made by GENETIX to Fstat may change the
     the sorting of the genotypes; GENETIX stores individual names
     whereas Fstat does not; Genepop chooses a sample's name from the
     name of its last genotype; etc.

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

     an object of the class 'genind'

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

     Thibaut Jombart t.jombart@imperial.ac.uk

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

     Belkhir K., Borsa P., Chikhi L., Raufaste N. & Bonhomme F.
     (1996-2004) GENETIX 4.05, logiciel sous Windows TM pour la
     génétique des populations. Laboratoire Génome, Populations,
     Interactions, CNRS UMR 5000, Université de Montpellier II,
     Montpellier (France). 

     Pritchard, J.; Stephens, M. & Donnelly, P. (2000) Inference of
     population structure using multilocus genotype data. _Genetics_,
     *155*: 945-959

     Raymond M. & Rousset F, (1995). GENEPOP (version 1.2): population
     genetics software for exact tests and ecumenicism. _J. Heredity_,
     *86*:248-249 

     Fstat (version 2.9.3). Software by Jerome Goudet.
     http://www2.unil.ch/popgen/softwares/fstat.htm

     Excoffier L. & Heckel G.(2006) Computer programs for population
     genetics data analysis: a survival guide _Nature_, *7*: 745-758

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

     'import2genind', 'read.genetix', 'read.fstat', 'read.structure',
     'read.genepop'

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

     import2genind(system.file("files/nancycats.gtx",
     package="adegenet"))

     import2genind(system.file("files/nancycats.dat",
     package="adegenet"))

     import2genind(system.file("files/nancycats.gen",
     package="adegenet"))

     import2genind(system.file("files/nancycats.str",
     package="adegenet"), onerowperind=FALSE, n.ind=237, n.loc=9, col.lab=1, col.pop=2, ask=FALSE)

