Genetic Marker operators

Setting marker positions

!MMAP s 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). s (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 to Morgans). Further details are provided in the User Guide.

 ChrAadd !G 10 !MM 1 ...

Dominance variables

!DOM A 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, 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 qtl().

  ChrAdom !DOM ChrAadd

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