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
.