isPoly-methods           package:adegenet           R Documentation

_A_s_s_e_s_s _p_o_l_y_m_o_r_p_h_i_s_m _i_n _g_e_n_i_n_d/_g_e_n_p_o_p _o_b_j_e_c_t_s

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

     The simple function 'isPoly' can be used to check which loci are
     polymorphic, or alternatively to check which alleles give rise to
     polymorphism.

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

     ## S4 method for signature 'genind':
     isPoly(x, by=c("locus","allele"), thres=1/100)
     ## S4 method for signature 'genpop':
     isPoly(x, by=c("locus","allele"), thres=1/100)

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

       x: a genind and genpop object

      by: a character being "locus" or "allele", indicating whether
          results should indicate polymorphic loci ("locus"), or
          alleles giving rise to polymorphism ("allele").

   thres: a numeric value giving the minimum frequency of an allele
          giving rise to polymorphism (defaults to 0.01).

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

     A vector of logicals.

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

     Thibaut Jombart t.jombart@imperial.ac.uk

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

     data(nancycats)
     isPoly(nancycats,by="loc", thres=0.1)
     isPoly(nancycats[1:3],by="loc", thres=0.1)
     genind2df(nancycats[1:3])

