orderMarkers               package:qtl               R Documentation

_F_i_n_d _a_n _i_n_i_t_i_a_l _o_r_d_e_r _f_o_r _m_a_r_k_e_r_s _w_i_t_h_i_n _c_h_r_o_m_o_s_o_m_e_s

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

     Establish initial orders for markers within chromosomes by a
     greedy algorithm, adding one marker at a time with locations of
     previous markers fixed, in the position giving the miniminum
     number of obligate crossovers.

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

     orderMarkers(cross, chr, window=7, use.ripple=TRUE, error.prob=0.0001,
                  map.function=c("haldane","kosambi","c-f","morgan"),
                  maxit=4000, tol=1e-4, sex.sp=TRUE, verbose=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 consider. 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.

  window: If 'use.ripple=TRUE', this indicates the number of markers to
          include in the sliding window of permuted markers.  Larger
          numbers result in the comparison of a greater number of
          marker orders, but will require a considerable increase in
          computation time.

use.ripple: If TRUE, the initial order is refined by a call to the
          function 'ripple'.

error.prob: Assumed genotyping error rate used in the final estimated
          map.

map.function: Indicates the map function to use in the final estimated
          map.

   maxit: Maximum number of EM iterations to perform in the final
          estimated map.

     tol: Tolerance for determining convergence in the final estimated
          map.

  sex.sp: Indicates whether to estimate sex-specific maps in the final
          estimated map; this is used only for the 4-way cross.

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

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

     Markers within a linkage group are considered in order of
     decreasing number of genotyped individuals.  The first two markers
     are placed in an arbitrary order.  Additional markers are
     considered one at a time, and each possible placement of a marker
     is compared (with the order of the previously placed markers taken
     as fixed) via the number of obligate crossovers (that is, the
     minimal number of crossovers that would explain the observed
     data).  The marker is placed in the position giving the minimal
     number of obligate crossovers.  If multiple positions give the
     same number of obligate crossovers, a single location (among those
     positions) is chosen at random.

     If 'use.ripple=TRUE', the final order is passed to 'ripple' with
     'method="countxo"' to refine the marker order.  If
     'use.ripple=TRUE' and the number of markers on a chromosome is <=
     the argument 'window', the initial greedy algorithm is skipped and
     all possible marker orders are compared via 'ripple'.

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

     The output is a cross object, as in the input, with orders of
     markers on selected chromosomes revised.

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

     Karl W Broman, kbroman@biostat.wisc.edu

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

     'formLinkageGroups', 'ripple', 'est.map', 'countXO'

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

     data(listeria)
     pull.map(listeria, chr=3)
     revcross <- orderMarkers(listeria, chr=3, use.ripple=FALSE)
     pull.map(revcross, chr=3)

