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HelixTree provides tools for the design and analysis of family-based association studies through the capabilities of the PBAT software package developed by Dr. Christoph Lange of Harvard University ( www.hsph.harvard.edu/faculty/ChristophLange.html).

NOTE: These submenu items will only be available if you are licensed to use PBAT.

3.7.1 Family Based Data Import

To perform family-based association analysis in HelixTree you must first import your data from a known family-based source. HelixTree will then create spreadsheets with PBAT analysis options available.

See 4.5 for information about importing data for family-based analyses. Also see 23 for information about performing PBAT family-based analyses.

3.7.1.1 Running PBAT CNV Analysis

To perform PBAT CNV analysis using HelixTree, select the PBAT->PBAT CNV Analysis menu option. This menu option will open a dialog that allows you to select a LogR DSF file, a pedigree spreadsheet, and various analysis options for the CNV analysis. See 23.5 for more information on performing the analysis.

3.7.2 PBAT Power Calculations

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The menu options in the PBAT->PBAT Power Calculation group invoke a dialog through which you can set the parameters for, and start PBAT Power Calculations. The Tools->PBAT Power Calculation->Use Default Parameters menu item will open the dialog using the default parameters for the calculations. If you would like to start with a set of parameters from a previous calculation, highlight the PBAT Power Calculation results node that has the parameters that you wish to use, and select the Tools->PBAT Power Calculation->Use Parameters From Selected Node menu option. See 23.3 for a more detailed description of the dialog and calculations.

NOTE: These submenu items will only be available if you are licensed to use PBAT.