The Q-K Mixed Model process tests for association between various types of traits and SNP genotypes or alleles from a single SNP at a time while adjusting simultaneously for population structure and family relatedness (Yu et al. 2006). You must already have computed the Q and K matrices. Two types of analyses can be performed: an ANOVA based on SNP genotypes or a regression testing for a linear trend of SNP alleles. P-values from these tests, with adjustments applied if requested, are plotted along the marker map.
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.
A second, optional, data set is the Annotation Data Set. This data set contains information, such as gene identity or chromosomal location, for each of the markers. The annotation data set used in this example, the samplemap.sas7bdat data set, was computer generated and identifies markers, locations, and gene identities. A portion of this data set is illustrated below. This data set is a tall data set; each row corresponds to a different marker.
Note: The top-to-bottom order of the rows in the annotation data set matches the left-to-right order of the columns in the input data set. This correspondence is required for markers to be matched appropriately.
Both data sets are 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 Mixed Model output documentation for detailed descriptions and guides to interpreting your results.