ghimport.sas

The SAS Software macro ghimport.sas reads in the dump-sas.ibd and genehunter.ped files (as named in this example) and creates a SAS Software dataset suitable for analysis with qms2.sas. ghimport.sas is fully documented in Chapter ghimport.sas. The easiest way to use ghimport.sas is calling it using the SAS Software option mautosource. This allows the replacement of the ghimport.sas macro without changing the SAS Software script.

	  options mautosource sasautos=('$HOME/sas/qms2');
	

The ghimport.sas is then called using a SAS Software macro reference. Macros are called by preceding the name of the macro with a "%". Any variables to be passed to the macro are placed inside "( )" and separated by a ",". To allow for default values, all macro variables in ghimport.sas are called using the form variable=value. To improve readability, a macro call can be broken across multiple lines.

In Example 3-4 the macro is called with all of the available arguments. IBDs will be read from the file dump-sas.ibd, and the phenotypes will be read from genehunter.ped. The phenotype file contains 10 markers and uses the value "-99" to represent missing data. The data will NOT be read in as-is (i.e. there are probands in the dataset and double entry will be performed). The output will be saved the the dataset sample in the qtl library.

	  %ghimport(ibdfile=dump-sas.ibd,
	            phenfile=genehunter.ped,
	            markers=10,
	            missing=-99,
	            asis=0,
	            outdata=qtl.sample);
	

The code snippet in Example 3-4 will import data from the files dump-sas.ibd and genehunter.ped and save it into the temporary dataset ibdphen.