Output Description

Linkage Disequilibrium

Running this process for the GeneticMarkerExample sample setting generates the tabbed Results window shown below. Refer to the Linkage Disequilibrium 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:

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.

The following tabs are generated by this process:

• LD Decay: This tab shows how the LD, in terms of whatever measure, Dprime or CorrCoeff, has been selected for the Measure for LD Decay Plot option, decays over distance.
• Haplotype Frequency Charts: When the Create haplotype frequency charts check box has been checked, this tab displays frequency charts of the possible haplotypes at each pair of markers for which LD was calculated.
• Annotation Group Plots/All Markers Plots (Linkage Disequilibrium): When there are multiple annotation groups (chromosomes or genes, for example), each Annotation Group Plots tab displays a lower triangular plot of the LD p-values for pairs of markers in that annotation group. A contour plot of the measure, if any, selected for the Measure for LD Decay Plot option is also shown.

If there is only one annotation group or no annotation group variable is specified, this tab displays these one or two plots for all marker pairs.

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:

• Launch Interactive LD Plots for R^2

There is either one button for each annotation group, or one for all markers if no annotation groups have been specified. In this example, there are two annotation groups: CandGene 1 and CandGene 2.

Each button opens a window with a HaploView-style LD plot for that annotation group (chromosome, for example) along with a legend displaying the color gradient for the values for R2 (also called CorrCoeff2, the square of the correlation coefficient). Markers are spaced uniformly in the triangular plot, but have lines drawn to their chromosomal position.

You can click on selected blocks and use the drill-down buttons at the bottom of the plot to annotate and name selected blocks, zoom into selected blocks of interest, and change the color theme.

Screenshots of the plot and legend for one annotation group are shown below:

Note: The values plotted along the x-axis of the LD plot refer to the chromosomal position of the markers, as shown at the top of the plot.

Output Data

This process generates the following output data sets:

Matrix of CorrCoeff2 Data Set(s): This data set contains the square of the LD correlation coefficients in matrix form (that is, one row and one column per marker in the annotation group). One data set is generated for each annotation group.

Note: These data sets are generated only if the Create data sets of CorrCoeff2 in matrix format check box has been checked.

LD Statistics Data Set: This data set contains all of the marker statistics computed by the Linkage Disequilibrium process. 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 _lds. Note: This data set is generated and placed in the specified output folder every time this process is run. However, a link to this data set is not surfaced in the Results window

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

General

• Click to reveal the underlying data table associated with the current tab.
• Click to reopen the completed process dialog used to generate this output.
• Click to generate a pdf- or rtf-formatted report containing the plots and charts of selected tabs.
• Click to close all graphics windows and underlying data sets associated with the output.