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:
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.
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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.
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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.
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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).
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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.
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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.
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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.
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GenBank Nucleotide
: Select points or rows and click
to opens a browser window directed to a GenBank Nucleotide search for the selected molecular entities.
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UniGene Database
: Select points or rows and click
to access information from the Unigene database for selected genes or markers
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AceView Database
: Select points or rows and click
to access information from the ACEView database for selected genes or markers.
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dbSNP
: Select points or rows and click
to open a browser window directed to an NCBI dbSNP search for the pair of SNPs associated with the particular instance of this button.
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Click
to reveal the underlying data table associated with the current tab.
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Click
to reopen the completed process dialog used to generate this output.
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Click
to generate a
pdf
- or
rtf
-formatted report containing the plots and charts of selected tabs.
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Click
to close all graphics windows and underlying data sets associated with the output.
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