The
Calculate Square Root of Matrix
process outputs a data set containing columns of the square root of a matrix calculated by Singular Value Decomposition. The input matrix is defined by the columns of the
Input Data Set
specified as Matrix Variables. This analytical process can be used to calculate the SVD root of a custom kinship matrix that was not computed using the
Relationship Matrix
process for input into the
Q-K Mixed Model
process. When used for this purpose, the input
K matrix
variables must form a square, symmetric matrix that define the
covariance
of the
random effect
that you want to fit in the
Q-K
mixed model. The square root computation of the estimated kinship covariance matrix is necessary for accurately fitting the correct covariance structure according to how the
Q-K Mixed Model
process computes the
model
. This process is necessary only if the matrix to be used as the
K
random component was calculated in an external program, otherwise it can be calculated in the
Relationship Matrix
process. The output
K
matrix square root variables can then be specified in the
Q-K Mixed Model
process to ensure that the correct covariance structure is formed.
Note
: The output data set containing the square root matrix variables from this process should be merged with the
SNP
data set in preparation for using the
Q-K Mixed Model
process. If the input data set already contains columns of SNP data, these
variables
should be retained
in the output data set.
One data set is required to run the
Calculate Square Root of Matrix
process. This
Input Data Set
, contains all of the marker data. The
morocco_kmatrix.sas7bdat
data set, shown below, represents a 193 x 193 matrix of
Identity By Descent
(IBD) values calculated between individuals from genome-wide SNP using data from a study of gene
expression
variation and SNP
associations
in southern Morocco (Idaghdour, Czika,
et al
., 2010)
For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
The output of the
Calculate Square Root of Matrix
process includes one output data set that contains the square root of the input matrix and a set of
Action Buttons
. The data set is accessed from a tabbed
Results
window.
This process was run for the data sets shown above. The
morocco_kmatrix_svd.sas7bdat
output data set (shown below) represents the square root of the
morocco_kmatrix.sas7bdat
input data set and is ready for use as input for the
Q-K Mixed Model
process.
The action button surfaced on the
Results
window, enables you to launch the
Q-K Mixed Model
process with the results of the
Calculate Square Root of Matrix
process preloaded, for further analysis.