Running this process for the
MoroccoExample
sample setting generates the tabbed
Results
window shown below. Refer to the
K Matrix Compression
process description for more information. Output from the process is organized into tabs. Each tab contains one or more plots, data panels, data filters, and so on. that facilitate your analysis.
The
Results
window contains the following panes:
This pane provides you with a space to view individual tabs within the
Results
window. Use the tabs to access and view the output plots and associated data sets.
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Results (K Matrix Compression)
: This tab contains all the results of
K matrix
compression. The appearance of this tab depends on the
Compression Method
specified. When
Optimized
compression (the default selection) is specified the tab displays a plot of
model
criteria versus compression levels (on the
x
-axis). When
Interactive
compression is specified, the JMP hierarchical platform is surfaced, enabling you to specify your own level of compression. When
Automated
compression is specified, a
Results
tab is not generated. Instead, the process automatically returns a data set with the compressed matrix.
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SAS Output
: This is a text-based output directly from PROC CLUSTER and either SAS PROC MIXED or SAS PROC GLIMMIX for fitting the
mixed model
for K matrix compression level. Refer to the documentation for
SAS PROC MIXED
or
SAS PROC GLIMMIX
for more information.
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Note
: This tab is generated only when
Optimized
has been specified as the
Compression Method
and the
List every model fit
check box has been checked.
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: This button is displayed when
Optimized
has been specified as the
Compression Method
and the
Create PARMS statement from optimal model covariance parameter estimates
check box has been checked (default settings). Click this button to launch a JMP window containing the PARMS statement options used to fix the
covariance
parameters in the
Q-K Mixed Model
process.
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: This button is displayed when
Interactive
has been specified as the
Compression Method
. Click this button once you have chosen your level of compression (using the JMP interactive Hierarchical Clustering platform), to re-run the compression process in
Automated
mode to produce the compressed
K
matrix.
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Compressed K Matrix from K Matrix Compression
: This data set (defined by suffix
_kc
) is generated when either
Optimized
or
Automated
is specified as the
Compression Method
. It contains the computed compressed
K
matrix merged with the SNP Input Data set and any
variables
to retain specified on the
dialog
and is used as input for the
Q-K Mixed Model
process.
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Covariance Parameters from K Matrix Compression
: This data set (defined by suffix
_kcv
) is created when the
Create data set of covariance parameter estimates for every model fit
check box is checked and
Optimized
has been specified as the
Compression Method
. It contains the covariance parameter estimates for the genetic effect and model
residual
for each level of compression tested. It is useful to see how the estimates change and vary across compression levels.
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For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
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Q-K Mixed Model
: Click
to launch the
Q-K Mixed Model
process with the compressed
K
matrix (listed in the
Output Data
Pane above) preloaded as input.
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Click
to reveal the underlying data table associated with the current tab.
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Click
to reopen the completed process dialog used to generate this output.
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Click
to generate a
pdf
- or
rtf
-formatted report containing the plots and charts of selected tabs.
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Click
to close all graphics windows and underlying data sets associated with the output.
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