Running this process using the GeneticMarkerExample sample setting generates the tabbed Results window shown below. Refer to the 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.
The Results window contains the following panes:
Tabs
This pane enables you to access and view the output plots and associated data sets on each tab. Use the drop-down menu to view the tab in the Tab Viewer pane, open the tab in a new window, or remove the tab and its contents from the Tab Viewer pane.
The following tabs are generated by this process:
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Summary Chart: When there are multiple annotation groups (chromosomes or genes, for example), this tab displays the number of significant markers in each annotation group for each test. Separate bar charts are shown for each BY group when any BY variables are specified. This tab is open by default.
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Manhattan Plot: When there are multiple annotation groups (chromosomes or genes, for example), this tab displays a scatter plot of the p-values across all annotation groups.
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Annotation Group Results: When there are multiple annotation groups (chromosomes or genes, for example), a separate Results tab with an overlay plot of p-value by chromosome location is created for each annotation group. If the Calculate trend odds ratios check box was checked, this tab also contains a Volcano Plotof p-value by log odds ratio for all markers.
In this example, there are two annotation groups (CandGene 1, and CandGene 2) and, thus two Annotation Group Results tabs (CandGene 1 Results and CandGene 2 Results).
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All P-Value Plots: When there are multiple annotation groups (chromosomes or genes, for example), the All P-Value Plots tab shows all the p-value plots from the Annotation Group Results tabs in a single display.
Note: When an annotation group variable is not specified or there is only one annotation group, the tab is named P-Value Plot and contains an overlay plot of p-value by chromosome location for all markers.
Volcano Plot(s): This tab displays a scatter plot of p-value by the Estimate of Minor Allele Genotype Effect for all markers, colored by Annotation Group, when the trend test is performed. When the Output genotype LS means and diffs check box is checked, this tab includes scatter plots of p-value by the LS diffs between genotypes 0 and 1, and genotypes 0 and 2.
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SAS Output : This is a text-based output directly from either SAS PROC MIXED or SAS PROC GLIMMIX for fitting the mixed model for each marker. Refer to the documentation for SAS PROC MIXED or SAS PROC GLIMMIX for more information.
Drill Downs
Action buttons provide you with an easy way to drill down into your data. The following action buttons are generated by this process:
Note: This option is available only when two or more Trait Variables are specified.
Output Data
This process generates the following data set(s):
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Genotype Residual Data Set: This data set contains input data set merged with columns of residuals from each genotype test model (each SNP, for example) and is generated when the Genotype test is performed and the Output residuals from every model check box is checked. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _org. Click to view the data set.
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Genotype LSMeans and Differences Data Set: This data set contains the LS means and diffs estimates and associated statistics for each regression model and is generated when the Output genotype LS means and diffs check box is checked. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _lsm. Click to view the data set.
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Genotype Parameter Estimate Data Set: This data set contains the estimates and test statistics for the fixed effects included in each regression model testing for association, including the marker genotype treated as a categorical variable, and is generated when the Genotype test is performed. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _peg. Click to view the data set.
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Genotype Covariance Parameter Estimate Data Set: This data set contains the estimates for the covariance parameters (random effects) included in each regression model testing for association, including the residual. This data set is generated when the Genotype test is performed and random effects are specified. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _cpg. Click to view the data set.
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Trend Residual Data Set: This data set contains input data set merged with columns of residuals from each trend test model (each SNP, for example). This data set is generated when the Trend test is performed. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _ort.Click to view the data set.
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Trend Parameter Estimate Data Set: This data set contains the estimates and test statistics for the fixed effects included in each regression model testing for association, including the numeric marker genotype treated as a continuous variable, and is generated when the Trend test is performed. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _pet.Click to view the data set.
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Trend Covariance Parameter Estimate Data Set: This data set contains the estimates for the covariance parameters (random effects) included in each regression model testing for association, including the residual. This data set is generated when the Trend test is performed and random effects are specified. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _cpt. Click to view the data set.
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P-value Data Set: This data set contains all the columns from the annotation data set, plus the test statistics and p-values from the tests performed. This data set can be used as the annotation data set for subsequent processes to accumulate results from multiple processes into a single data set. The name of this data is set is given by the Output File Prefix, or input data set name if none given, with the suffix _sta. Click to view the data set.
For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.
Tab Viewer
This pane provides you with a space to view individual tabs within the Results window.
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.
