LD tagSNP Selection

Running this process for the GeneticMarkerExample sample setting generates the tabbed Results window shown below. Refer to the LD tagSNP Selection 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:

•	All Results: This tab displays a plot with SNP locations along the x-axis and a separate plot for each annotation group, if selected. Each SNP is either given a blue plus symbol or a red circle indicating whether it has been selected as tag SNP or not, respectively.

If any BY variables were selected, a separate set of plots is shown for each BY group.

•	Annotation Group Results: When an annotation group variable has been selected, this tab displays a plot, or set of plots if any By Variables, like that described above for the given annotation group.

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.

Output Data

This process generates the following output data set:

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tagSNP Indicator Data Set: When the Create tagSNP subset indicator variable check box has been checked, this data set contains the variables from the annotation data set along with variables indicating what bin, if any, each SNP has been assigned to, the size of the bin, a variable indicating whether the SNP is a tagSNP for the bin, and an indicator for including that SNP in a subset. This last variable randomly selects a tagSNP from each bin if there are more than one tagSNPs for the bin, so that the SNPs with a value of 1 in that column can be used as a subset of SNPs representing the data. The button described below can be used to automatically create this subset.

For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.

Launch Follow-up Process

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Subset and Reorder Genetic Data: Click to launch and run the Subset and Reorder Genetic Data process using the same input data set as for LD tagSNP Selection and the tagSNP Indicator data set as the annotation data set preloaded as input, with tagSNPSubset = 1 entered in the Filter to Include Markers field, to create subset data sets only including the selected tagSNPs.

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.