Output | Genetics | Multiple SNP-Trait Association

Multiple SNP-Trait Association
Running this process using the MoroccoExample sample setting generates the tabbed Results window shown below. Refer to the Multiple SNP-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 (Multiple SNP-Trait 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 (Multiple SNP-Trait Analysis): 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 SNP 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.
SAS Output: This tab displays the output from the SAS procedure(s) used for the analysis.
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.
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.
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.
View Venn Diagram of Significant Markers by Trait for the Test Below: Click on the button corresponding to the desired association test to view a Venn diagram of genes with significant association according to that test for the specified traits. Use this Venn diagram, generated either with all of the genes or those in a particular annotation plotting group, to identify the genes 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):
Parameter estimate data for Multiple-Locus Reg: When the Multiple-Locus Regression test is performed, this data set contains the estimates and test statistics for the fixed effects included in each regression model testing for association, including the marker genotypes. The name of this data is set is given by the Output Data Set Prefix, or input data set name if none given, with the suffix _mpe.Click Open to view the data set.
Covariance parameter data for Multiple-Locus Reg: When the Multiple-Locus Regression test is performed and random effects are specified, this data set contains the estimates for the covariance parameters (random effects) included in each mixed model testing for association, including the residual. The name of this data is set is given by the Output Data Set Prefix, or input data set name if none given, with the suffix _mcp. Click Open to view the data set.
Parameter estimate data for PCA Reg: When the PC Regression test is performed, this data set contains the estimates and test statistics for the fixed effects included in each PC regression model testing for association, including the principal components created from the SNP genotypes. The name of this data is set is given by the Output Data Set Prefix, or input data set name if none given, with the suffix _mpep. Click Open to view the data set.
Covariance parameter data for PCA Reg: When the PC Regression test is performed and random effects are specified, this data set contains the estimates for the covariance parameters (random effects) included in each PC mixed model testing for association, including the residual. The name of this data is set is given by the Output Data Set Prefix, or input data set name if none given, with the suffix _mcpp. 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.