Calculate Genetic Predictors

Available Data

This lists data structures appropriate to the current input field. Double-click on a name to copy it to the current input field; alternatively, you can type the name directly into the input field. If data has been stored in a QTL workbook then only the data structures present within that workbook will be displayed in the available data, otherwise all the current data within GenStat will be displayed. When data are present within the QTL workbook you can right-click on the available data list to open a shortcut menu where you can change between displaying data only within the workbook and all data within GenStat.

Marker genotype scores

A pointer specifying the marker scores. The pointer should contain a set of factors (one for each marker) where each factor has the same labels representing the genotype scores and the labels are all in the same order:

a, b, u	for a doubled haploid population.
a, h, u or b, h, u	for a backcross population.
a, b, h, c, d, u	for a F2 or recombinant inbred lines population.

where a = AA, b = BB, h = AB, c = B* (not AA), d = A* (not BB), and u or - = missing.

Linkage groups

A factor defining the different linkage groups (or chromosomes).

Marker names

A text defining the marker names for each set of genotype scores.

Position within linkage groups

A variate specifying the positions of each marker within the linkage groups.

Type of population

A list of population types. Select F2 for an F2 population, BC1 for a backcross population, DH for a double-haploid population and RILn for a population of recombinant inbred lines. When RILn is selected the number of generations for the population can be supplied using the number of generations option.

Save Genetic Predictors and associated information

This allows you to save the genetic predictors and associated information for the predictors.

Additive effects in	pointer	saves the additive effects in a pointer to a set of variates where each variate contains the values for a virtual marker.
Dominance effects in	pointer	saves the dominance effects for an F2 population. Note that these can only be saved within this menu and are not used in any other menus.
Linkage groups	factor	linkage groups for each virtual marker.
Position within linkage group	variate	position within linkage group for each virtual marker.
Marker names	text	save the virtual marker names.

Action Buttons

Run	Run the analysis.
Cancel	Close the menu without further changes.
Options	Opens a dialog where additional options and settings can be specified.
Defaults	Set the menu settings back to the default settings. Clicking the right mouse on this button produces a shortcut menu where you can choose to set the menu using the currently stored defaults or the GenStat default settings.