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'.

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

     a character string or vector

_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'

