The
Kinship Matrix
process creates a matrix containing either
kinship (coancestry) coefficients
or covariance coefficients (coefficients of relationship) between pairs of related individuals. It is required that the
pedigree
observations
are ordered in the
Input Data Set
so that individuals are defined before being used as the parents of other individuals, and it is required that any individual listed as the parent of another individual be included in the data set.
Calculated coefficients can be used as
random effects
in order to analyze family data in an
association
setting, for example in the
Marker-Trait Association
or
SNP-Trait Association
processes that can accommodate random effects.
One data set is required to run the
Kinship Matrix
process. The first, the
Input Data Set
, contains all of the marker data. The sample data set used in the following example, the
samplegmdata
data set, was computer generated as described in
Sample Genetic Marker Data
. It consists of 1000 rows of individuals with 130 columns corresponding to data on these individuals. Marker data is presented in the two-column format. 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.
For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
Output from this process is accessed from a
Results
window. Refer to the
Kinship Matrix
output documentation for detailed descriptions and guides to interpreting your results.