Marker-Trait Association

Running this process using the GeneticMarkerExample_KMatrix sample setting generates the tabbed Results window shown below. Refer to the Marker-Trait 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 : 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 : 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.

•

Annotation Group Results : 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. 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 : 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.

•	All Trends Odds Ratio Plots : : If the Calculate trend odds ratios check box was checked and there are multiple annotation groups (chromosomes or genes, for example), this tab shows all the odds ratio volcano plots .

•	SAS Output : This tab displays the SAS output from the MIXED, GLIMMIX, LOGISTIC, or PHREG procedure in SAS/STAT, which is run to fit the model . Information about estimates for fixed effects and covariance parameter estimates is included in this output as well as fit statistics for the model.

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:

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

Note : This action button is not available if either multiple traits or any By Variables are selected.

•	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.

•	UniGene Database : Select points or rows and click UniGene Database to access information from the Unigene database for selected genes or markers

•	AceView Database : Select points or rows and click AceView Database to access information from the ACEView database for selected genes or markers.

•	Plot Trait by Genotype : Select markers from the p -value plots and click Plot Trait by Genotype to view each marker's genotype distribution for each of the Trait Variables values.

Note : This action button is available only when numeric genotypes are specified.

•

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.

Output Data

This process generates the following data set(s):

•

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.

•

Genotype Covariance Parameter Estimate Data Set : This data set contains the estimates for the covariance parameters ( K matrix and/or random effects ) included in each regression model testing for association, including the residual . This data set is generated when the Genotype test is performed and random effects are specified. 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 _cpg . Click Open to view the data set.

•

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.

•

Trend Covariance Parameter Estimate Data Set : This data set contains the estimates for the covariance parameters ( K matrix and/or random effects) included in each regression model testing for association, including the residual. This data set is generated when the Trend test is performed and random effects are specified. 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 _cpt . Click Open to view the data set.

•

P -value Data Set: This data set contains all the columns from the annotation data set , plus the test statistics and p -values from the tests performed. This data set can be used as the annotation data set for subsequent processes to accumulate results from multiple processes into a single data set. 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 _mta . 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.