Plot

Running the %TPLOT macro creates a window displaying a graphical representation of the marker test results.

Figure 12.1 shows an example of the TPLOT results window.

Figure 12.1 Results Window for TPLOT Macro
Results Window for TPLOT Macro

This plot contains a grid of points with symbols that represent the -values for various marker tests. Colors and shapes of the data points are used to symbolize -value ranges. The Show Info About Points button on the toolbar enables the -values to be displayed. If you hold down the left mouse button while positioning the mouse pointer on any point in the plot, the pop-up window appears for off-diagonal points, displaying the two markers being tested for linkage disequilibrium and the -value of the test; the window displays the marker and its -values for the HWE test and marker-trait association test for points on the diagonal, as shown in Figure 12.1.

Disequilibrium Tests

The -values from the linkage disequilibrium tests between all pairs of markers (or all markers within a certain range of each other) are represented by the color of the squares on the off-diagonal of the plot. For the points on the diagonal, the results from the Hardy-Weinberg equilibrium test are displayed instead of the linkage disequilibrium tests since the same marker locus is on the horizontal and vertical axes.

The three ranges of -values that correspond to different colored symbols in the plot are as follows:

Red

[0, 0.01]

Orange

(0.01, 0.05]

Yellow

(0.05, 1]

The disequilibrium test -values that are plotted can be provided by the output data set from PROC ALLELE, or by a user-created data set meeting the requirements described in the Syntax: TPLOT Macro section.

Marker-Trait Association Tests

Points on the diagonal also display -values from marker-trait association tests, using the shape of the symbol to correspond to two categories of -values, significant and not significant. The significance level is set to 0.05 by default, but can be modified using the ALPHA= option in the %TPLOT macro. Thus, for a significance level of , the following shapes represent the following ranges:

Plus

tplss04  [0, ]

Triangle

tplss03  (, 1]

Note that the square shape tplss05 of the off-diagonal points does not represent a marker-trait association -value since there are two different marker loci represented on the horizontal and vertical axes. These -values can be provided by the output data set of PROC CASECONTROL, PROC FAMILY, or PROC PSMOOTH. Alternatively, a user-created data set that meets the conditions described in the Syntax: TPLOT Macro section can be used.