SNP-SNP Interactions

Running this process using the MoroccoExample sample setting generates the tabbed Results window shown below. Refer to the SNP-SNP Interactions 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:

•	Results (SNP-SNP Interactions): This tab display a distribution of the p-values from any test performed, Genotype or Trend, along with a Data Filter to restrict the view to p-values from any Interaction Block Variables.

Drill Downs

Action buttons provide you with an easy way to drill down into your data. The following action button is generated by this process:

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View plot of input data for the selected interaction(s): Select points from the distributions and click on this button to view plots of the trait by genotypes at the two SNPs. The window containing these plots also has buttons for linking to the annotation website for the selected interaction pair when the process is run with an annotation accession variable specified.

Output Data

This process generates the following data set(s):

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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 Open 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 Open 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 Open 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 Open 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 Open 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 _ssi. Click Open to view the data set.

For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.

General

•	Click View Data to reveal the underlying data table associated with the current tab.

•	Click Reopen Dialog to reopen the completed process dialog used to generate this output.

•	Click Create Report to generate a pdf- or rtf-formatted report containing the plots and charts of selected tabs.

•	Click Close All to close all graphics windows and underlying data sets associated with the output.