Linkage Disequilibrium (LD) Decay

Select menu: Stats | QTLs (linkage/Association) | Genotypic Analysis | Linkage Disequilibrium (LD) Decay

Use this to estimate linkage disequilibrium (LD) between pairs of markers on a chromosome, by fitting a generalized linear model that uses one marker as predictor of the second marker. The association between markers is assessed by the deviance ratio between the models with and without the marker predictor. LD is not calculated between markers with a distance greater than the specified maximum distance set in the options.

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

You can set additional Options before running the analysis and store the results by clicking Store.

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 has the same labels representing the genotype scores and the labels are all in the same order.

Linkage groups

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

Position within linkage group

A variate specifying the positions within linkage group for each marker.

Relationship model

Specifies the model to account for genetic relatedness between genotypes.

Eigenanalysis	Infers the underlying genetic substructure in the population by retaining the most significant principal components from the molecular marker matrix – the scores of the significant axes are used as covariables in the mixed model, which effectively is an approximation to the structuring of the genetic variance covariance matrix by a coefficient of coancestry matrix (kinship matrix).
Subpopulation groupings	Provides a space to supply a factor of subpopulation groupings to be included in the mixed model.
Null	No correction is made for genetic relatedness.

Linkage groups to analyse

Specifies the linkage group to use in the analysis. This should be supplied using a level or label from the linkage group factor.

Action buttons

Run	Run the association analysis.
Cancel	Close the dialog without further changes.
Options	Opens a dialog where additional options and settings can be specified for the analysis.
Defaults	Reset options to the default settings. Clicking the right mouse on this button produces a pop-up menu where you can choose to set the menu using the currently stored defaults or the Genstat default settings.
Store	Opens a dialog to specify names of structures to store the results from the analysis.

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.