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Form Kinship Matrix

Select menu: Stats | QTLs (linkage/Association) | Genotypic Analysis | Form Kinship Matrix

Use this to form a kinship matrix of coancestries from marker scores. The coefficients of coancestries can be calculated using either the Dice similarity measure or by simple correlation. The kinship matrix can be used within a marker-trait association analysis using bi-allelic and multi-allelic markers.

  1. After you have imported your data, from the menu select
    Stats | QTLs (linkage/Association) | Genotypic Analysis | Form Kinship Matrix.
  2. Fill in the fields as required then click Run.

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.

Labels for genotypes

A text specifying labels for the genotypes used to label the rows (and columns) of the kinship matrix.

Save matrix in

Provides a space to specify the name of symmetric matrix to save the kinship matrix.

Action buttons

Run Form the kinship matrix.
Cancel Close the dialog without further changes.
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.

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.

See also

Updated on April 24, 2019

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