I Installing HelixTree and Acquiring Data
Part I
Installing HelixTree and Acquiring Data
1 Installing and Initializing HelixTree
1.1 Installation Overview
1.2 Release Notes
2 Welcome to HelixTree
2.1 Goals for this Chapter
2.2 Recursive Partitioning Primer
2.3 The HelixTree Basic Workflow
2.4 Tutorial 1: Performing the Basic Workflow in GUI Mode
2.5 Tutorial 2: Performing the Basic Workflow in Scripting Mode
2.6 Tutorial 3: Detailed Guide to a Standard Case/Control Association Study
3 Navigating the Main Screen
3.1 Main Screen Overview
3.2 Project Viewer Window
3.3 Navigator Nodes
3.4 The File Menu
3.5 The Tools Menu
3.6 The CNAM Menu
3.7 The PBAT Menu
3.8 The Help Menu
4 Importing Your Data Into HelixTree
4.1 General Considerations
4.2 Mathematical Considerations
4.3 Importing Data
4.4 Importing Copy Number Data
4.5 Importing Family-Based Data
5 Scripting and Other Integrated Statistical Tools
5.1 Integrated Tools Overview
5.2 The Python Shell Window
5.3 Running Scripts
5.4 Selecting a Script Server
5.5 Example Scripts
5.6 Scripting Reference
5.7 S-PLUS Integration
5.8 R Integration
5.9 PBAT Integration
6 Using the Spreadsheet Viewer
6.1 Spreadsheet Overview
6.2 Manipulating, Filtering and Preparing Data Using the Spreadsheet
6.3 The File Menu
6.4 The Edit Menu
6.5 The Analysis Menu
6.6 The Genetics Menu
6.7 The Help Menu
1.1 Installation Overview
1.2 Release Notes
2 Welcome to HelixTree
2.1 Goals for this Chapter
2.2 Recursive Partitioning Primer
2.3 The HelixTree Basic Workflow
2.4 Tutorial 1: Performing the Basic Workflow in GUI Mode
2.5 Tutorial 2: Performing the Basic Workflow in Scripting Mode
2.6 Tutorial 3: Detailed Guide to a Standard Case/Control Association Study
3 Navigating the Main Screen
3.1 Main Screen Overview
3.2 Project Viewer Window
3.3 Navigator Nodes
3.4 The File Menu
3.5 The Tools Menu
3.6 The CNAM Menu
3.7 The PBAT Menu
3.8 The Help Menu
4 Importing Your Data Into HelixTree
4.1 General Considerations
4.2 Mathematical Considerations
4.3 Importing Data
4.4 Importing Copy Number Data
4.5 Importing Family-Based Data
5 Scripting and Other Integrated Statistical Tools
5.1 Integrated Tools Overview
5.2 The Python Shell Window
5.3 Running Scripts
5.4 Selecting a Script Server
5.5 Example Scripts
5.6 Scripting Reference
5.7 S-PLUS Integration
5.8 R Integration
5.9 PBAT Integration
6 Using the Spreadsheet Viewer
6.1 Spreadsheet Overview
6.2 Manipulating, Filtering and Preparing Data Using the Spreadsheet
6.3 The File Menu
6.4 The Edit Menu
6.5 The Analysis Menu
6.6 The Genetics Menu
6.7 The Help Menu
