locus                  package:bqtl                  R Documentation

_L_o_o_k_u_p _l_o_c_i _o_r _e_f_f_e_c_t_s _f_o_r _g_e_n_e_t_i_c _m_o_d_e_l _f_o_r_m_u_l_a_s

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

     Convert numeric indexes to names of regressors for a genetic
     model. One or many genetic models can be specified through the use
     of this function.  It is used on the right hand side of a formula
     in the 'bqtl' function.

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

     locus(x, ..., scope, method, chromo, cM, ana.obj)
     add(x)
     dom(x)

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

       x: Typically an integer, an integer vector, or an array whose
          elements are integers. These index loci described in a
          'map.frame' object. 

          However, 'x' can also be a character string, vector, et
          cetera, in which case the elements must belong to
          'names(scope)'. 

     ...: Optional arguments (usually integers) to be used when
          'is.atomic(x)' is TRUE.  

 chromo : A chromosome number or 2 ordered numbers. The loci on the
          chromosome or in the range of chromosome numbers are used. If
          'chromo' is used, 'x' must not be used.

     cM : (Optional) map distance or two giving a location near a locus
          or range of locations from which loci will be included. If
          the one chromosome number is specified in 'chromo', 'cM' must
          be  ordered. If 'cM' is omitted, all loci on the
          chromosome(s) will be included.

   scope: (Optional and) Usually not supplied by the user.  Rather
          'bqtl' fills this in automatically.  A vector of regressor
          names, like the 'reg.names' component returned by
          'make.analysis.obj'.

  method: (Optional and)  Usually not supplied by the user. Like
          'scope', 'bqtl' takes care of filling this in with "BC1",
          "F2", et cetera as appropriate.

 ana.obj: Usually not specified by the user. This is the
          'analysis.object' to be used to lookup loci if a 'chromo'
          argument is used.

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

     'locus' is used in the model formula notation of 'bqtl', possibly
     more than once, and possibly with regressors named in the usual
     manner.  'locus' is intended to speed up the specification and
     examination of genetic models by allowing many models to be
     specified in a shorthand notation in a single model formula.  The
     names of genetic loci can consist of marker names, names that
     encode chromosome number and location, or other shorthand
     notations.  The names of terms in genetic models will typically
     include the names of the locus and may prepend "add." or "dom." or
     similar abbreviations for the 'additive' and 'dominance' terms
     associated with the locus.

     When used as in 'bqtl( y ~ locus(34), my.analysis.obj )', it will
     look up the term or terms corresponding to the 34$^{th}$ locus.
     When this is passed back to 'bqtl', it is pasted into a text
     string that will become a formula and is subsequently processed to
     yield the fit for a one gene model.

     When used as in 'bqtl( y ~ locus(34,75,172), my.analysis.obj)' it
     looks up each term and returns a result to 'bqtl' that results in
     fitting a 3 gene model (without interaction terms). 

     When 'x' is a vector or array, the processing typically returns
     pieces character strings for many model formulas.  'bqtl(y ~
     locus(26:75), ...)' results in a list of 50 different one gene
     model fits from 'bqtl' for the terms corresponding to the 26th
     through the 75th variables.  ' bqtl(y ~
     locus(cbind(c(15,45,192),c(16,46,193))),...)' returns two three
     gene models.  And more generally, whenever 'is.array(x)' is TRUE,
     the columns (or slices) specify ' dim(x)[1]/length(x)' different
     models. 

     The 'chromo' argument performs a lookup of loci on the chromosome
     via the function 'map.index'. If 'cM' is also given, the locus
     nearest that location is used. If two values are given for 'cM'
     all loci in the range are used.

     'add(x)' and 'dom(x)' are alternatives that specify that only the
     _additive_ or _dominance_ terms in an F2 intercross.

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

     A character vector whose element(s) can be parsed as the right
     hand side of a model formula(s).

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

     Charles C. Berry cberry@ucsd.edu

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

     'configs', 'bqtl', and the examples there for a sense of how to
     use 'locus',  'make.analysis.obj' for the setup that encodes the
     marker map and the marker information.

