Calculate Number of Recombinations

Select menu: Stats | QTLs (linkage/Association) | Map Construction | Calculate Number of Recombinations

Use this to calculate the expected number of recombinations and the recombination frequencies between markers given the marker scores of each marker.

After you have imported your data, from the menu select
Stats | QTLs (linkage/Association) | Map Construction | Calculate Number of Recombinations.
Fill in the fields as required then click Run.

You can set additional Options before running the calculation and Store the results.

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 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.

Marker names

A text specifying the names for each marker.

Parent information

The parent information should be supplied within a pointer to a set of texts (one for each parent).

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
CP for outcross populations.

Method

Specifies the method to use for calculating the number of recombinations using either a Two point or Multi-point method. If the order of the markers is not available then the Two point method must be used.

Initial order or markers

When the Multi-point method is selected this can be used to supply a variate containing the initial order of the markers.

Action buttons

Run	Calculate the number of recombinations.
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.