| locus {bqtl} | R Documentation |
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.
locus(x, ..., scope=<see below>,method=<see below>) add(x,...) dom(x,...) bqtl( y ~ PVV.4 + locus(14,17), my.analysis.object ) bqtl( y ~ locus(14,17) * locus(133,245), my.analysis.object ) bqtl( y ~ add(14) +dom(27), my.f2.object )
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.
|
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. |
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.
add(x) and dom(x) are alternatives that specify that only
the additive or dominance terms in an F2 intercross.
A character vector whose element(s) can be parsed as the right hand side of a model formula(s).
Charles C. Berry cberry@ucsd.edu
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.