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.
covar(x)a character string or vector
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.
Charles C. Berry cberry@ucsd.edu
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'.
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
locus, add, dom,
configs