GWAS Meta-Analysis

Running this process using the StudyExample sample setting generates the tabbed Results window shown below. Refer to the GWAS Meta-Analysis 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 (GWAS Meta-Analysis): 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 (GWAS Meta-Analysis): 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.

•	Chromosome Results: When there are multiple chromosomes, a separate Chromosome Results tab is created with an overlay plot of the meta-analysis p-value by chromosome location for the markers on that Chromosome Results tab.

Note: In the example shown here, there are three Chromosome Results tabs: CHR 2 Results, CHR 7 Results, and CHR 11 Results.

•	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.

•	Heterogeneity Statistics: This tab displays the distribution of the heterogeneity statistics Cochran's Q, the p-value for Cochran's Q, and I2 across all markers. This tab is generated when either inverse variance method for combining p-values has been selected using the Method to Use parameter.

•	Volcano Plot(s): This tab displays a scatter plot of overall p-value by overall effect estimate colored by annotation group when either inverse variance method for combining p-values has been selected.

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.

•	Forest Plot: Click Forest Plot to view forest plots for selected SNPs.

The forest plots show the effect estimates from each study and their confidence intervals, with a diamond centered at the overall estimate with width extending the length of the overall confidence interval. Sizes of markers at the effect estimate convey the weight used for that study.

This button is surfaced when either inverse variance method for combining p-values has been selected using the Method to Use parameter.

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.