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:
Tab Viewer
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.
The following tabs are generated by this process:
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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.
: 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.
Output Data
This process generates the following output data sets:
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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.
For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.
Launch Follow-up Processes
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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.
General
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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.
