Calculate Genetic Predictors

Select menu: Stats | QTLs (linkage/Association) | Genotypic Analysis | Calculate Genetic Predictors

Use this to calculate conditional genotypic probabilities at specific chromosome positions. These genetic predictors can be used within a QTL analysis. If data structures have been stored within the QTL data space then the names of the structures will be automatically entered in the relevant input fields.

After you have imported your data, from the menu select
Stats | QTLs (linkage/Association) | Genotypic Analysis | Calculate Genetic Predictors.
Fill in the fields as required then click Run.

You can set additional Options before running the analysis.

Available data

This lists data structures appropriate to the current input field. Double-click a name to copy it to the current input field or type the name. If data has been stored in a QTL data space then only the data structures present within that data space will be displayed in the Available data, otherwise all the current data within Genstat will be displayed. When data are present within the QTL data space you can right-click on the Available data list to open a shortcut menu where you can change between displaying data only within the data space 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 contains the labels for the alleles separated by the ‘/’ character. For example, if the allele for parent 1 was a and the allele for parent 2 was b the labels for a factor for a marker should be as follows:

a/a, b/b, -/-	For a doubled haploid population.
a/a, a/b, -/-	For a backcross population.
a/a, b/b, a/b, a/-, b/-, -/-	For a F2, recombinant inbred lines or backcrossed inbred lines population.

Where – = missing. The parent information for each marker should be supplied using the Parental information field.

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.

Parental information

A pointer specifying the parental information for the marker genotype scores.

Labels for parents

A text specifying labels for the parents that correspond to the text structures in the parental information pointer.

Type of population

A list of population types. Select as follows:

F2 for an F2 population
BC1 for a backcross population
DH for a double-haploid population
RILn for a population of recombinant inbred lines
BCxSy for a population of backcross inbred lines
CP for outcross populations.

When RILn is selected the number of generations for the population can be supplied using the Number of generations option. When BCxSy is selected the number of backcrosses and selfings for the population can be supplied using the Number of backcrosses and Number of selfings options respectively.

Save genetic predictors and associated information

This lets you 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.
Additive effects 2nd parent in	Pointer	Saves the additive effects for the 2nd parent for a CP population 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 or CP population.
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	Saves the virtual marker names.
Marker locus indicator	Variate	Saves a logical indicating the positions of the original marker names within the virtual marker names.

Action buttons

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

Action Icons

	Pin	Controls whether to keep the dialog open when you click Run. When the pin is down the dialog will remain open, otherwise when the pin is up the dialog will close.
	Restore	Restore names into edit fields and default settings.
	Clear	Clear all fields and list boxes.
	Help	Open the Help topic for this dialog.