Find Associated Variables

Find Associated Variables

This function is applicable to a genotype-by-marker two-way table or a QTL mapping dataset.

Under Association, click Find Associated Testers of….
An input box will appear, asking for the probability level for a marker to be considered as 'associated' with the target marker. Put a number between 0 and 0.5, and click OK. A panel will appear above the biplot.
Click the drop-down arrow by the textbox, and select the target marker, and then click Find.
An input box will appear, asking if you want to use any traits/markers as covariate. Since the default answer is No, just click OK.
The following changes to the biplot will occur:
Traits/markers that do not meet the criteria are deleted;
The target marker is indicated by a larger and underlined font;
Only trait/marker labels are shown to focus on the relationships among traits/markers (the genotypes are hidden and can be called back by clicking Full Names or Show Both under the main menu View);
Trait/marker vectors (lines from biplot origin to the trait labels) are drawn to facilitate visualization of the relations among them.
Traits may be manually deleted by clicking Data Manipulation/Run a Subset by…/Removing any Testers.
The linear map of the markers can be brought up by clicking Biplot Analysis/Linear Map of Testers.

Interpretation:

If the retained markers have a maximum angle near 90°, the markers are from more than one linkage group. You could repeat the process using more stringent criteria to delete less linked markers. Note: there can be more than one linkage group on a single chromosome.
Within a linkage group, the order and relative distance among the markers on the biplot and the linear map should be roughly consistent with their positions on the chromosome.