countXO                 package:qtl                 R Documentation

_C_o_u_n_t _n_u_m_b_e_r _o_f _o_b_l_i_g_a_t_e _c_r_o_s_s_o_v_e_r_s _f_o_r _e_a_c_h _i_n_d_i_v_i_d_u_a_l

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

     Count the number of obligate crossovers for each individual in a
     cross, either by chromosome or overall.

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

     countXO(cross, chr, bychr=FALSE)

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

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

     chr: Optional vector indicating the chromosomes to investigate.
          This should be a vector of character strings referring to
          chromosomes by name; numeric values are converted to strings.
           Refer to chromosomes with a preceding '-' to have all
          chromosomes but those considered.  A logical (TRUE/FALSE)
          vector may also be used.

   bychr: If TRUE, return counts for each individual chromosome; if
          FALSE, return the overall number across the selected
          chromosomes.

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

     For each individual we count the minimal number of crossovers that
     explain the observed genotype data.

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

     If 'bychr=TRUE', a matrix of counts is returned, with rows
     corresponding to individuals and columns corresponding to
     chromosomes. 

     If 'bychr=FALSE', a vector of counts (the total number of
     crossovers across all selected chromosomes) is returned.

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

     Karl W Broman, kbroman@biostat.wisc.edu

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

     'ripple'

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

     data(hyper)
     plot(countXO(hyper))

