Marker Properties

Running this process for the GeneticMarkerExample sample setting generates the tabbed Results window shown below. Refer to the Marker Properties 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, remove the tab and its contents from the Tab Viewer pane, or open the output data set(s) used to generate the plots and charts illustrated on the tab.

The following tabs are generated by this process:

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Summary Chart (Marker Properties) : When there are multiple annotation groups ( chromosomes or genes, for example), this tab displays the number of significant markers in each annotation group for the Hardy-Weinberg equilibrium (HWE) test. Separate bar charts are shown for each BY group when any BY variables are specified. This tab is open by default.

•	Manhattan Plot : When there are multiple annotation groups (chromosomes or genes, for example), this tab displays a scatter plot of the HWE p-values across all annotation groups.

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Annotation Group Results : When there are multiple annotation groups (chromosomes or genes, for example), a separate Results tab with an overlay plot of HWE p -value by chromosome location as well as distributions of minor allele frequency (MAF) and missing genotype proportion for the markers in that annotation group.

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 ).

•	All P-Value Plots : When there are multiple annotation groups (chromosomes or genes, for example), the All P-Value Plots tab shows all the HWE p -value plots from the Annotation Group Results tabs in a single display.

Note : When an annotation group variable is not specified or there is only one annotation group, the tab is named P-Value Plot and contains an overlay plot of HWE p -value by chromosome location for all markers.

•	All Distributions : This tab shows all the distributions from the Annotation Group Results tabs in a single display. When an annotation group variable is not specified or there is only one annotation group, a single set of distribution results for MAF and missing genotype proportion is displayed.

•	Individual Missing Genotype Proportion : This tab displays a distribution of the proportion of missing genotypes by individual.

•	Cell Plot : When the Create cell plot check box has been checked, this tab displays a cell plot representation of the individuals' genotypes at all markers.

•	Marker Frequencies : When the Create frequency charts check box has been checked, this tab displays allele and genotype frequency charts for each marker.

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:

•	Create Subset Genotype and Annotation Data Sets : Select points from the p -value plots and click Create Subset Genotype and Annotation Data Sets to open the Subset and Reorder Genetic Data process to create the subset data sets.

Note : This action button is not available if any By Variables are selected.

•	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.

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Filter Markers/Individuals Based on the Criteria Below: Use this data filter to create subset data sets. Enter cutoffs for MAF, proportion of missing genotypes, or HWE p -values based on distributions and plots to subset markers from both the genotype and annotation data sets for analysis. You can also enter a cutoff for individuals' proportion of missing genotypes in order to remove individuals that have excessive missing genotypes from the genotype data set.

Enter the desired values in the appropriate text boxes and click OK to generate the new subset data set.

Output Data

This process generates the following output data sets:

Marker Statistics Data Set: This data set contains all the columns from the annotation data set, plus various marker statistics and the test statistics and p -values from the HWE test. This can be used as the annotation data set for subsequent processes to accumulate results from multiple processes into a single data set. 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 _hwe . Click Open to view the data set.

Numerically Coded Genotypes Data Set: This data set contains the input data set with marker variables converted to numeric genotypes coded as 0, 1, or 2, representing the count of minor alleles (or non- major alleles if the marker is multiallelic) the genotype comprises. It is generated when the Create data set with numerically coded genotypes check box has been checked.

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.