Genetic Marker operators
Setting marker positions
assigns Haldane map positions (s) to marker variables and imputes
values to the markers where they have missing values.
This transformation will normally be used on a !G n factor
where the n variables
are the marker states for n markers
in a linkage group in map
order and coded [-1,1] (backcross) or [-1,0,1] (F2 design).
(length n+1) should
be the n marker positions relative to a left
telomere position of zero, and an extra value being the length of the
linkage group (the position of the right telomere).
The length (right telomere) may be omitted in which case the
last marker is taken as the end of the linkage group.
The positions may be given in Morgans or centiMorgans
(if the length is greater than 10, it will be divided by 100 to convert
Further details are provided in the
ASReml User Guide.pdf
ChrAadd !G 10 !MM 1 ...
is used to form dominance covariables
from a set of additive marker covariables previously
declared with the !MM
marker map qualifier. It assumes the argument A is an existing group
of marker variables relating to a linkage group
defined using !MM which represents additive marker variation
coded [-1, 0, 1] (representing marker states aa,
and AA) respectively.
It is a group transformation which takes the [-1,1] interval values, and calculates
(|X|-0.5)*2 i.e. -1 and 1 become one, 0 becomes -1.
The marker map is also copied and applied to this model term
so it can be the argument in a
ChrAdom !DOM ChrAadd
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