Recombination and Linkage Groups

Running this process using the BC1_example sample setting generates the tabbed Results window shown below. Refer to the Recombination and Linkage Groups 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.

Tab Viewer

This pane provides you with a space to view individual tabs within the Results window. Use the tabs to access and view the output plots and associated data sets.

•	Linkage Group Results: This tab displays the recombination matrix and linkage group assignment for markers in your experimental population using the JMP Hierarchical Clustering Platform. This tabbed pane will be shown only if the Plot heatmaps for linkage groups option is checked.

•	Linkage Groups and Segregation: This tab displays a plot of p-values from testing segregation distortion each marker and distribution plot(s) of markers belonging to each linkage group as well as markers belonging to Framework Map groups (if a Framework Map was specified).

Note: This tab will not be shown if AIL or IRIL is selected as the Cross Type and no values have been entered for the Expected Segregation Ratios for AA AB BB parameter on the dialog.

Action Buttons

Action buttons provide you with an easy way to drill down into your data. The following action buttons are generated by this process:

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Save Current Linkage Group Membership: Click and hold the diamond () and slide it left or right to determine the number of linkage groups. Click Save Current Linkage Group Membership to save the current number of linkage groups as determined based on the location of the Diamond tool () to the output data set.

Note: This action button is available only when you choose the Interactive Hierarchical Clustering linkage group method.

•	Exclude Markers and Rerun Analysis: Click Exclude Markers and Rerun Analysis to rerun recombination and linkage grouping while excluding any selected markers.

You can interactively select markers that are show segregation distortion or do not fit well in linkage groups and remove them with this action button.

Output Data

This process generates the following data set(s):

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Linkage Groups and Recombination Matrix from Linkage Groups: This is output data set contains the computed recombination matrix between all markers and the linkage group assignment. This data set is ready to be used for the Linkage Map Order process to continue with linkage map construction. This data set contains any interactive results, unless the option to Plot heatmaps for linkage groups check box is unchecked.

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 Processes

•	Linkage Map Order: Click Linkage Map Order to launch the Linkage Map Order process with the output linkage groups and recombination data set and the original input genotype data set preloaded as input.

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.