Output Description
Haplotype Estimation
Running this process using the GeneticMarkerExample sample setting generates the tabbed Results window shown below. Refer to the Haplotype Estimation 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:
| • | Summary Chart: When there are multiple annotation groups (chromosomes or genes, for example), this tab displays the number of significant markers in each annotation group for each 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 p-values across all annotation groups. |
| • | 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).
| • | All P-Value Plots: When there are multiple annotation groups (chromosomes or genes, for example), the All P-Value Plots tab shows all the 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 p-value by chromosome location for all markers.
LD P-Value Plot: This tab is surfaced only when the Test allelic association for LD box is checked. It shows the results of linkage disequilibrium among alleles present in each haplotype.
Output Data
This process generates the following data set(s):
| • | Phase assignment Data Set: This data set contains for each individual in the input data set, a row for all possible haplotype pairs for each marker window and the corresponding probability. This data set is generated when the Create Phase Assignment Data Set check box has been checked. |
The haplotype pairs can be filtered by setting a minimum probability for the pair to be included in the data set in the Phase Assignment Probability Cutoff option. Alternatively, if the Output most probable haplotype pair only check box is checked, only the single most probable haplotype pair is included for each individual in a marker window.
This data set also includes any By Variables and selected Phase Assignment ID Variables and thus can be used as the input data set for Haplotype Trend Regression 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 _hph.
| • | Haplotype Frequency Estimates Data Set: This data set contains the frequency estimate for each haplotype at each marker window. This data set is generated when the Create data set containing haplotype frequency estimates check box has been checked. |
When the Test allelic association for LD check box has been checked, frequencies under both the null hypothesis (H0) of no LD (the product of the allele frequencies) and under the alternative hypothesis (H1) that accounts for LD are included in the output. When this option is not checked, only the estimated frequencies under the alternative hypothesis are included (calculated using the EM or StepEM algorithm).
This data set can be used as the input data set for the htSNP Selection process or as the Haplotype Frequency Data Set in the Haplotype Trend Regression 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 _hfr.
| • | Haplotype-Trait Association Data Set: This data set includes a chi-square test for different haplotype frequencies between the two values of the trait variable. This data set is generated when a Binary Trait Variable has been selected and the Test Individual Haplotypes check box has been checked, |
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 _hta.
For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.
Launch Follow-up Processes
| • | Haplotype Trend Regression: Click to launch the Haplotype Trend Regression process with the Phase Assignment data set and the Haplotype Frequency Estimates data set preloaded as input. |
| • | htSNP Selection: Click to launch the htSNP Selection process with the Haplotype Frequency Estimates data set preloaded as input. |
Tab Viewer
This pane provides you with a space to view individual tabs within the Results window.
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. |