Compatibility check

Select menu: Stats | QTLs (linkage/Association) | Data Manipulation | Compatibility Check

Use this to perform a compatibility check of qtl data. It can be used to remove genotypes that have greater than certain percentage of missing values. When genotypes are excluded this menu can also be used to exclude the corresponding values in the trait variate, the genotypes factor, the kinship matrix and the subpopulations factor.

After you have imported your data, from the menu select
Stats | QTLs (linkage/Association) | Data Manipulation | Compatibility Check.
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.

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
AMP for an association mapping population.

Marker scores

The Data to replace field specifies a pointer for 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. A new structure name should be entered in the Save in field to save the new marker scores.

Linkage groups

The Data to replace field specifies a factor for the linkage groups (or chromosomes). A new structure name should be entered in the Save in field to save the new linkage groups (or chromosomes).

Position within linkage group

The Data to replace field specifies a variate for the positions within linkage group for each marker. A new structure name should be entered in the Save in field to save the new positions within linkage group for each marker.

Marker names

The Data to replace field specifies a text for the names of each marker. A new structure name should be entered in the Save in field to save the new marker names.

Genotype labels

The Data to replace field specifies a text of the labels for the genotypes that correspond with the labels for the genotypes for the phenotypic means. This data structure is used to ensure that there is correct matching for the genotypes between genotypic and phenotypic data. A new structure name should be entered in the Save in field to save the genotype labels.

Parental information

For F2, DH1, BC1, RIL, BCxSy and CP populations the Data to replace field specifies a pointer to the parental information. A new structure name should be entered in the Save in field to save the new parental information.

Labels for parents

For F2, DH1, BC1, RIL, BCxSy and CP populations the Data to replace field specifies a text for the labels for the parents. A new structure name should be entered in the Save in field to save the labels for the parents.

Kinship matrix

For association mapping populations the Data to replace field specifies a symmetric matrix for a kinship matrix. A new structure name should be entered in the Save in field to save the new kinship matrix.

Subpopulation factor

For association mapping populations the Data to replace field specifies a factor for a subpopulation factor. A new structure name should be entered in the Save in field to save the new subpopulation factor.

Traits

The Data to replace field specifies a list of variates for the quantitative trait (phenotypic) means for each genotype. The number of structures in the Save in list should match those from within the Data to replace list.

Genotype factor

The Data to replace field specifies a factor for the genotypes. A new structure name should be entered in the Save in field to save the new genotypes.

Environments factor

The Data to replace field specifies a factor for the environments. A new structure name should be entered in the Save in field to save the new environments.

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 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.

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.