formLinkageGroups            package:qtl            R Documentation

_P_a_r_t_i_t_i_o_n _m_a_r_k_e_r_s _i_n_t_o _l_i_n_k_a_g_e _g_r_o_u_p_s

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

     Use pairwise linkage information between markers (as calculated by
     'est.rf' to partition markers into linkage groups.

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

     formLinkageGroups(cross, max.rf=0.25, min.lod=3, reorgMarkers=FALSE,
                       verbose=FALSE)

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

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

  max.rf: Maximum recombination fraction for placing two markers in the
          same linkage group (see Details).

 min.lod: Minimum LOD score for placing two markers in the same linkage
          group (see Details).

reorgMarkers: If TRUE, the output is a cross object, like the input,
          but with the markers organized into the inferred linkage
          groups.  If FALSE, the output is a table indicating the
          initial chromosome assignments and the inferred linkage group
          partitions.

 verbose: If TRUE, display information about the progress of the
          calculations.

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

     Two markers are placed in the same linkage group if the estimated
     recombination fraction between them is <= 'max.rf' and the LOD
     score (for the test of the rec. frac. = 1/2) is >= 'min.lod'.  The
     transitive property (if A is linked to B and B is linked to C then
     A is linked to C) is used to close the groups.

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

     If 'reorgMarkers=FALSE' (the default), the output is a data frame
     with rows corresponding to the markers and with two columns: the
     initial chromosome assignment and the inferred linkage group. 
     Linkage groups are ordered by the number of markers they contain
     (from largest to smallest).

     If 'reorgMarkers=TRUE', the output is a cross object, like the
     input, but with the markers reorganized into the inferred linkage
     groups.  The marker order and marker positions within the linkage
     groups are arbitrary.

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

     Karl W Broman, kbroman@biostat.wisc.edu

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

     'est.rf', 'orderMarkers'

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

     data(listeria)
     listeria <- est.rf(listeria)
     result <- formLinkageGroups(listeria)
     tab <- table(result[,1], result[,2])
     apply(tab, 1, function(a) sum(a!=0))
     apply(tab, 2, function(a) sum(a!=0))

