Output Description

Rare Variant Association

Running this process using the MoroccoExample sample setting generates the tabbed Results window shown below. Refer to the Rare Variant 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:

•

Summary Chart (Rare Variant Association): When there are multiple annotation groups (chromosomes, for example), this tab displays the number of significant annotation groups (typically genes) for each annotation plotting 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: When there are multiple annotation plotting groups (chromosomes, for example), this tab displays a scatter plot of the p-values across all annotation plotting groups.

•

Annotation Plotting Group Results: When there are multiple annotation plotting groups (chromosomes, for example), a separate Results tab is created for each annotation plotting group with an overlay plot of p-value by the chromosome location of the first SNPs in each annotation analysis group (typically gene).

Note: In the example shown here, an annotation plotting group results tab is generated for each chromosome. These tabs are enclosed in the blue rectangle in the figure above.

•

All P-Value Plots: When there are multiple annotation plotting groups (chromosomes, for example), the All P-Value Plots tab shows all the p-value plots from the Annotation Plotting Group Results tabs in a single display.

Note: When an annotation plotting group variable is not specified or there is only one annotation plotting group, the tab is named P-Value Plot and contains an overlay plot of p-value by chromosome location of the first SNP in each annotation analysis group for all analysis groups.

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:

•

GenBank Nucleotide: Select points or rows and click GenBank Nucleotide to opens a browser window directed to a GenBank Nucleotide search for the selected molecular entities.

•

dbSNP: Select points or rows and click dbSNP to open a browser window directed to an NCBI dbSNP search for the pair of SNPs associated with the particular instance of this button.

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.