This page should get you up and running with HPlus in as short a time as possible.
For further information on particular topics, links to other help pages are included, or
you can go back and select from the contents page.
When HPlus is first run, the main window looks like this:
To begin with, you need to load some kind of genetic marker data into the application. This
can either be in the form of a project you previously saved with HPlus, or you
can import a data set from a text file. Both of these options
are available in the File menu.
Once data is loaded, the main window will look something like this:
To the left of the window is the task bar which contains buttons to perform various
operations on the data. When data is first imported, the only task is to start the analysis.
On the right of the window are several frames. The top frame shows a summary of
the markers for the current data set. If the markers are SNPs, they are presented in a standardized
format:
- 0 - Homogeneous wild type
- 1 - Heterozygous
- 2 - Homogeneous variant
Below this frame are the location and covariate frames. These will be empty unless your imported data
set included some location and covariate information. The location frame will allow you to segment
the data prior to analysis. For example, if your data set included information on the gene in which
each marker resides, you would be able to select to segment by gene. Then when the analysis was run,
it would run once for each gene, only working on the markers present in that particular gene. In this
way, by choosing location variables, you can work on many combinations of the same markers. The covariate
frame will allow you to select from the available covariates and decide which are to be included and
corrected for in the analysis, and which subset of those should be included for gene-environment
interaction. Note that a covariate can only be included for interaction if it has already been
selected for inclusion in the analysis.
The final frame at the bottom lists the different 'sheets' of
information that can be viewed. Clicking on one of these buttons will display the relevant
sheet:
- Allele Freq: lists the allele frequencies for each marker
- Geno Freq: lists the genotype frequencies for each marker
- Hardy-Weinberg: shows the results of testing for Hardy-Weinberg equilibrium
- Results: shows the analysis results. This button is only visible if the analysis has been run.
Each of the allele, genotype and Hardy-Weinberg sheets has an 'export' button in the action panel on the
left allowing the information to be exported to a text file.
When an analysis has been performed, the main window will look something like this:
Now the frame on the left shows the following buttons:
- Visualization: shows plots and figures in a separate window relevant to the type of data that was analyzed
- Inferred Haplotypes: shows the inferred diplotypes (haplotype pairs) for each individual in the data set
- Change Ref...: Allows selection of which haplotype to use as the reference haplotype. Change the number in the box above the button.
The number indicates which haplotype, in frequency order, should be used as the reference. Frequency order is the order
of the haplotypes in the initial analysis before the reference was changed. Improvements in the reference selection interface
are to come.
Results can be exported using the 'Save
Results' option in the file menu. Also the project can be saved in a native format
to be reopened later by HPlus. Just use the 'Save Project' option in the File menu.
The right hand frame shows the haplotype frequencies and covariate statistics (if
any) for the current analysis. If an iterative analysis was used, or the data
was segmented into groups of markers, there will be multiple pages of results. To
select the results page to view, just choose from the drop-down menu which is located
in the bottom frame with the 'Input Data' and 'Output Data' buttons.
© 2003 Fred Hutchinson Cancer Research Center
Quantitative Genetic Epiedmiology
