htSNP Selection

Running this process using the GeneticMarkerExample sample setting generates the tabbed Results window shown below. Refer to the htSNP 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.

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:

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All Results (htSNP Selection): This tab displays for each annotation group an overlay plot, or set of plots if BY variables have been specified, with circles at the location of the markers that have been selected as a set of htSNPs on the x-axis, and the value of the selected criterion, either PDE or RSQH (specified using the Criterion for Evaluating Sets of htSNPs parameter), on the y-axis for that set.

•	Annotation Group Results: 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 of the first marker in the marker windows.

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).

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 data set(s):

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HTSNP Indicator Data Set: This data set contains the variables from the annotation data set plus an htSNP Indicator variable (htSNPInd) that contains a 1 for SNPs that are in the best set of htSNPs for that set/window of markers, 0 for those included in the search but not selected as htSNPs, and missing (.) for the markers not included in the search (due to low frequency for the haplotype that they occur in, for example).

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.