covar                  package:bqtl                  R Documentation

_T_r_e_a_t _l_o_c_u_s _a_s _c_o_v_a_r_i_a_t_e

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

     Sometimes it is helps speed computations to linearize the
     likelihood
 or at least a part of it w.r.t. the locus allele
     values. Both
 'Haley-Knott regression' and 'composite interval
     mapping' use this
 approach. `covar' provides a mechanism for
     creating formula
 objects that specify such linearizations.

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


     covar(x,...,scope=<<see below>>, method=<<see below>>)

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

       x: The name of a locus (except for F2 designs, when it is the
          name of an effect like 'add.m.32') or any argument of the
          sort that 
 `locus' allows.

     ...: If `x' evaluates to a single value, then additional
 atomic
          elements may be included as with `locus'.

   scope: Not supplied by the user. see locus

  method: Not supplied by the user. see locus

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

     The function `covar' actually only returns `x'. The real
 work is
     done by a `covar' function that is hidden inside of
 `bqtl', where
     the arguments are parsed as for `locus'. Each
 of the return
     values from `locus' is prefixed by "covar(" and
 suffixed by ")".
     If `x' is a name of a locus or effect, then
     `paste("covar(",deparse(x),")")' is returned. Later, when
 `bqtl'
     calls `lapadj', terms like `covar(PVV4.1)' are
 recognized as
     requiring a linearization w.r.t. effect 'PVV4.1'.

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

     Charles C. Berry cberry@ucsd.edu

_R_e_f_e_r_e_n_c_e_s:

     HALEY, C. S. and S. A. KNOTT, 1992  A simple regression method for
      mapping quantitative trait loci in line crosses using flanking
     markers. Heredity 69:315-324.

     Knapp SJ, Bridges WC, and Birkes D. Mapping quantitative trait
     loci
 using molecular marker linkage maps. Theoretical and Applied
     Genetics
 79: 583-592, 1990.

     ZENG, Z.-B., 1994 Precision mapping of quantitative trait
 loci.
     Genetics 136:1457-1468

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

     `locus', `add', `dom',
 `configs'

