comparegeno               package:qtl               R Documentation

_C_o_m_p_a_r_e _i_n_d_i_v_i_d_u_a_l_s' _g_e_n_o_t_y_p_e _d_a_t_a

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

     Count proportion of matching genotypes between all pairs of
     individuals, to look for unusually closely related individuals.

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

     comparegeno(cross, what=c("proportion","number","both"))

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

   cross: An object of class 'cross'.  See 'read.cross' for details.

    what: Indicates whether to return the proportion or number of
          matching genotypes (or both).

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

     A matrix whose (i,j)th element is the proportion or number of
     matching genotypes for individuals i and j.

     If called with 'what="both"', the lower triangle contains the
     proportion and the upper triangle contains the number.

     If called with 'what="proportion"', the diagonal contains missing
     values.  Otherwise, the diagonal contains the number of typed
     markers for each individual.

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

     Karl W Broman, kbroman@biostat.wisc.edu

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

     'nmissing'

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

     data(listeria)

     output <- comparegeno(listeria)

     # image of the proportions
     n.ind <- nind(listeria)
     image(1:n.ind, 1:n.ind, output, col=gray((0:99)/99),
           breaks=seq(0,1,len=101))

     # histogram 
     hist(output, breaks=150, prob=TRUE,
          xlab="Proportion of matching genotypes")
     rug(output)

