Plot :: SAS/Genetics(TM) 13.1 User's Guide

Plot

Subsections:

Disequilibrium Tests
Marker-Trait Association Tests

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

Figure 10.1 shows an example of the TPLOT results window.

Figure 10.1: Results Window for TPLOT Macro

This plot contains a grid of points with symbols that represent the $p$ -values for various marker tests. Colors and shapes of the data points are used to symbolize $p$ -value ranges. The Show Info About Points button on the toolbar enables the $p$ -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 $p$ -value of the test; the window displays the marker and its $p$ -values for the HWE test and marker-trait association test for points on the diagonal, as shown in Figure 10.1.

Disequilibrium Tests

The $p$ -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 $p$ -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 $p$ -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 $p$ -values from marker-trait association tests, using the shape of the symbol to correspond to two categories of $p$ -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 $\alpha$ , the following shapes represent the following ranges:

Plus: [0, $\alpha$ ]
Triangle: ( $\alpha$ , 1]

Note that the square shape tplss05 of the off-diagonal points does not represent a marker-trait association $p$ -value since there are two different marker loci represented on the horizontal and vertical axes. These $p$ -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.