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. |
See also
- Options for choosing which results to display
- QTL data space for using data in QTL menus
- QTL analysis using menus
- QMATCH procedure in command mode