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 the
K 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.