Pleiotropic Association

Running this process using the GeneticMarkerExample_KMatrix sample setting generates the tabbed Results window shown below. Refer to the Pleiotropic Association 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 (Pleiotropic Association): 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.

•	Manhattan Plot (Pleiotropic Association): 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 for each trait and for the MANOVA test.

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Annotation Group Results (Pleiotropic Association): 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 for each trait and for the MANOVA test. 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).

•	All P-Value Plots (Pleiotropic Association): 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 for each trait and for the MANOVA test.

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:

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View Venn Diagram of Significant Markers by Trait for the Test Below: Click either Genotype or Trend to view a Venn diagram showing significant association according to that test for the individual traits and the MANOVA test, either for all markers or those in a particular annotation group, so you can easily identify what markers are significant for one or more traits.

Note: This option is available only when two or more Trait Variables are specified.

The following is a Venn diagram of the Genotype test at all markers:

Output Data

This process generates the following data set(s):

•	Genotype MANOVA Data Set: This data set contains the statistics for each type of MANOVA statistic for each genotype test. 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 _pmg. Click Open to view the data set.

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Genotype LSMeans Data Set: This data set contains the LS means estimates and associated statistics for each regression model and is generated when the Output genotype LS means 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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Trend MANOVA Results Data Set: This data set, which is generated when the trend test is performed, contains the statistics for each type of MANOVA statistic when treating the numeric genotype as a continuous variable: Wilks' lambda, Pillai's trace, Hotelling-Lawley trace, and Roy's greatest root. 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 _pmt. 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 counts of each allele in the genotype treated as a continuous variable. 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 _pet. 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.

Tab Viewer

This pane provides you with a space to view individual tabs within the Results window.

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.