Running this process using the GeneticMarkerExample sample setting generates the tabbed Results window shown below. Refer to the Haplotype Q-K Mixed Model 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.
Tab Viewer
This pane provides you with a space to view individual tabs within the Results window. The following tabs are generated by this process:
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P-Value Plot Global: This tab includes a plot that displays the p-values (y-axis) from the global model (all haplotypes belonging to a window are tested together) for each window ID (x-axis).
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Model Fitness Plot Global: This tab includes a plot that displays model information criteria value (y-axis) from the global model (all haplotypes belonging to a window are tested together) for each window ID (x-axis).
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P-Value Plot Single: This tab includes a plot that displays the p-values (y-axis) from the single model (each haplotype belonging to a window is tested individually) for each haplotype ID (x-axis).
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Model Fitness Plot Single: This tab includes a plot that displays model information criteria value (y-axis) from the single model (each haplotype belonging to a window is tested individually) for each haplotype ID (x-axis).
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Volcano Plot Single: This tab displays a scatter plot of p-value (y-axis) by the Estimate of Haplotype Effect (x-axis) from the single model (each haplotype belonging to a window is tested individually).
Output Data
This process generates the following data set(s):
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Parameter estimates data for the global tests: This data set lists the global model test statistic for each window ID. The name of this data is set is given by the Output File Prefix, or input Phased Haplotypes Data Set name if none given, with the suffix _hgpe.
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Covariance parameter data for the global tests: This data set contains the estimates for the covariance parameters (random effects) included in each regression model for the global model, including the residual. This data set is generated only for the global model (all haplotypes belonging to a window are tested together) and when random effects are specified. The name of this data set is given by the Output File Prefix, or input Phased Haplotypes Data Set name if none given, with the suffix _hgcp.
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Residual data for the global tests: This data set contains columns of Individual ID Variables and residuals from the global model for each window ID. This data set is generated only for the global model (all haplotypes belonging to a window are tested together). The name of this data set is given by the Output File Prefix, or input Phased Haplotypes Data Set name if none given, with the suffix _hgor.
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Predicted data for the global tests: This data set contains columns of Individual ID Variables and predicted values from the global model for each window ID. This data set is generated only for the global model (all haplotypes belonging to a window are tested together). The name of this data set is given bythe Output File Prefix, or input Phased Haplotypes Data Set name if none given, with the suffix _hgop.
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Parameter estimates data for the single tests: This data set lists the F-statistics and associated probabilities for each of the estimated haplotypes on each window ID. The name of this data set is given by the Output File Prefix, or input Phased Haplotypes Data Set name if none given, with the suffix _hspe.
For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.
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.
