SequencesToGenind       package:adegenet       R Documentation(utf8)

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

     These functions take an alignement of sequences and translate SNPs
     into a genind object. Note that only polymorphic loci are
     retained.

     Currently, accepted sequence formats are:
      - DNAbin (ape package): function DNAbin2genind
      - alignement (seqinr package): to come...

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

     DNAbin2genind(x, pop=NULL, exp.char=c("a","t","g","c"), na.char=NULL, polyThres=1/100)

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

       x: an object containing aligned sequences.

     pop: an optional factor giving the population to which each
          sequence belongs.

exp.char: a vector of single character providing expected values; all
          other characters will be turned to NA.

 na.char: a vector of single characters providing values that should be
          considered as NA. If not NULL, this is used instead of
          'exp.char'.

polyThres: the minimum frequency of a minor allele for a locus to be
          considered as polymorphic (defaults to 0.01).

_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

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

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

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

     if(require(ape)){
     data(woodmouse)
     x <- DNAbin2genind(woodmouse)
     x
     genind2df(x)
     }

