Output Description

Missing Genotype by Trait Summary

Running this process for the GeneticMarkerExample sample setting generates the tabbed Results window shown below. Refer to the Missing Genotype by Trait Summary 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, remove the tab and its contents from the Tab Viewer pane, or open the output data set(s) used to generate the plots and charts illustrated on the tab.

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. 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), the Manhattan Plot tab displays a scatter plot of the p-values across all annotation groups..

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Annotation Group Results (Missing Genotypes by Trait Summary): When there are multiple annotation groups (chromosomes or genes, for example), a separate Results tab is created for each annotation group with an overlay plot of p-value by chromosome location, as well as an overlay plot and a distribution chart representation of missing genotype counts for each trait value.

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 and missing genotype count 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 HWE p-value by chromosome location for all markers.

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All Distributions: This tab shows all the distributions charts of number of missing genotypes for each trait value from the Annotation Group Results tabs in a single display.

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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Create Subset Genotype and Annotation Data Sets: Select points from the p-value plots and click Create Subset Genotype nd Annotation Data Sets to open the Subset and Reorder Genetic Data process to create the subset data sets.

Note: This action button is not available if any By Variables are selected.

Tab Viewer

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

General

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

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

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

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