The Q-K Model Fitness process can be used to fit different combinations of Q and K variables and model fitness information from each model, such as AIC, AICC, and BIC. This information is used to evaluate the best combination of Q and K to be used in the Q-K Mixed Model process for association tests.
One data set, the Input Data Set, which contains all of the marker data, is needed for this process. The sample data set used in the following example, the samplegmdata_numgeno_rm_pcm.sas7bdat data set, which was generated from the samplegmdata.sas7bdat described in Sample Genetic Marker Data, contains a root identity-by-descent (IBD) matrix computed for 60 computer-generated SNP genotypes by single value decomposition (SVD) from the Relationship Matrix process, a compressed IBD matrix from theK Matrix Compression process, a principal components matrix from the PCA for Population Stratification process, a coordinates matrix from the Multidimensional Scaling process, and a population membership probability, all merged with the original data. This data set is partially shown below. Note that this is a wide data set; markers are listed in columns, whereas individuals are listed in rows.
The samplegmdata_numgeno_rm_pcm.sas7bdat data set is included in the Sample Data folder that comes with JMP Genomics.For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.
The output generated by this process is summarized in a Tabbed report. Refer to the Q-K Model Fitness output documentation for detailed descriptions and guides to interpreting your results.