Syntax: TPLOT Macro :: SAS/Genetics(TM) 13.1 User's Guide

Syntax: TPLOT Macro

The %TPLOT macro has the following form:

%TPLOT (SAS-data-set, SAS-data-set, variable <,ALPHA=number>) ;

The first argument, SAS-data-set, specifies the name of the SAS data set that is the output data set from the ALLELE procedure (see Chapter 2), containing the linkage disequilibrium test and HWE test $p$ -values. A user-created data set can be used instead, but it is required to contain the variables Locus1 and Locus2 and a variable ProbChi containing the $p$ -values from the disequilibrium tests. The order in which the Locus1 and Locus2 variables are sorted is the order in which the values are displayed on the vertical and horizontal axes, respectively.

The second argument, SAS-data-set, specifies the name of the SAS data set that contains the $p$ -values for the marker-trait association tests. This data set can be the output data set from the CASECONTROL procedure, the FAMILY procedure, or the PSMOOTH procedure, or it can be created by the user. A user-created data set must contain a Locus variable for the values on the axes and a variable containing $p$ -values that is specified in the third argument, discussed in the following paragraph. The Locus variable must be in the same sorted order as the Locus1 variable in the data set named in the first argument.

The third argument, variable, names the variable that contains the marker-trait association $p$ -values in the SAS data set that is specified in the second argument.

The first three arguments are required. The following option can be used with the %TPLOT macro. The option must follow the three required arguments.

ALPHA=number: specifies the significance level for the marker-trait association test. This level is used as a cut-off for the $p$ -value range corresponding to the symbol shape on the plot. This number must be between 0 and 1. The default is ALPHA=0.05.