Summary Statistics for Markers

Select menu: Stats | QTLs (linkage/Association) | Data Exploration | Genotypic Data | Summary Statistics for Markers

Use this to generate descriptive statistics and diagnostic plots for molecular marker data. 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.

From the menu select
Stats | QTLs (linkage/Association) | Data Exploration | Genotypic Data | Summary Statistics for Markers.
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 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).

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.

Labels for genotypes

A text specifying labels for the genotypes that correspond with the labels for the genotypes for the phenotypic means. This data structure can be used to ensure that there is correct matching for the genotypes between genotypic and phenotypic data.

Parental information

For an F2, DH, RIL, BCxSy or BC1 population this specifies a pointer to a set of texts (one for each parent) containing the parent information. This information is required when displaying genotypes data plots.

Labels for parents

For an F2, DH, RIL, BCxSy or BC1 population this specifies a text containing id labels for the parental information. This information is required when displaying genotypes data plots.

Type of population

A list of population types. Select as follows:

F2 for an F2 population
BC1 for a backcross population
DH1 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.

Subset linkage groups

Defines a subset of the linkage groups to use for the analysis. This can be set to variate or a scalar of the group number(s) defining a subset of the levels of the linkage groups factor. If the linkage groups factor contains labels then a text defining a subset of its labels can be supplied. Alternatively, a comma separated list of group number(s) or labels can be supplied to specify the subset of linkage groups.

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.