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CIM search option
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| In the Create New MIM Model dialog: If enabled, click the Criterion… button to display the Set Composite Interval Mapping Control Parameters dialog box.
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| 1. | For the CIM Model field, specify the markers to be used as cofactors in the CIM analysis:
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| Model 1: All Marker Control. Use all the markers to control for the genetic background.
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| Model 2: Unlinked Marker Control. Use all unlinked markers to control for the genetic background.
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| Model 4: One Marker Control. This is an ad-hoc model. One marker from each chromosome (except for the chromosome on which we are testing) is used to control for the genetic background. The results of LRmapqtl are scanned, and the marker that showed the highest test statistic from each chromosome is used.
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| Model 5: Two Marker Control. Another ad-hoc model. Two markers from each chromosome are used to control for the genetic background. They are the top two markers as determined by LRmapqtl. In addition, all the other markers on the chromosome of the test position that are more than 10 cM away from the flanking markers are also thrown in. It may be ad-hoc, but tends to work best at this time. Selecting this model also requires you to fill in the Window size (cM) field (explained below).
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| Model 6: Standard Model. The default model that selects certain markers as control markers by using additional parameters: control marker number and window size. Selecting this model requires you to fill in extra fields on the dialog: Control marker numbers, Window size (cM), and Regression method selection (all explained below).
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| 2. | Click Set control markers manually if you do not want WinQTLCart to calculate the number of control markers. This will display a dialog box after you start the analysis so that you can manually select the control markers. Skip to the end of this topic for a description of this dialog box.
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| 3. | Control marker numbers. Enter the number of markers to control for the genetic background. WinQTLCart will use up to the number of markers entered here.
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| 4. | Window size (cM). Enter the window size in centiMorgans. The window size will block out a region of the genome on either side of the markers flanking the test site. Since these flanking regions are tightly linked to the testing site, if we were to use them as background markers we would then be eliminating the signal from the test site itself.
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| Recommendations
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| · | Model 6 is good for starting an analysis.
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| · | The default values of 5 for control markers and 10 for window size should be good starting points for Model 6.
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| · | Increasing the number of control markers will allow better resolution for mapping linked QTLs.
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| 5. | Regression method selection. Select a method:
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| 1: Forward Regression
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| 2: Backward Regression
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| 3: Forward & Backward
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| 6. | Probability for into:, Probability for out:.
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| 7. | If the trait number field is enabled, enter trait numbers and their ranges to be included in the model.
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| 8. | Click OK to close the dialog and return to the Create New MIM dialog.
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| 9. | Click the Criterion… button. The Set Threshold dialog appears. Enter a threshold value or click Default to accept the default value (recommended). Click OK to accept the value and close the dialog and return to the Create New MIM dialog.
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| 10. | Click the Start button to begin the search. The CIM form may display during the calculations. When the search is complete, the model is presented in the cells.
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| 11. | To manually edit the model:
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| · | Click Add QTL or Del QTL
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| · | Click on a cell and enter a new value in the Cell editing box. Click the Cell Update button to enter the new value.
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| 12. | Click OK to accept the parameters, close the dialog and return to the MIM form.
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