HelixTree Manual
Version 6.4.0
Copyright © 2000-2008
![[Picture]](splashHT.png)
HelixTree is a premier tool for extracting useful information from your data. At its heart is a sophisticated data analysis engine enhanced to support your ability to analyze genetics data. Golden Helix offers three ways for you to learn the capabilities and features of HelixTree.
The first and most immediate approach is this manual. In it you will find directions for installing HelixTree, tutorials on its use, and a comprehensive reference. You will need to read the section on installing the product. Also, we strongly recommend that you read the tutorials.
We recognize the difficulties learning any new skill from a book or manual no matter how well it is written. So, as a second approach to learning about HelixTree, we strongly recommend that you visit our web site at http://www.goldenhelix.com and sign up for a web-based seminar. The seminar can be set up to accommodate your schedule and its content can be tailored to meet your specific needs. The time spent in the seminar has proven to be a very effective way for new users to jump start their productivity with HelixTree and seasoned users to quickly acclimate to new features.
Finally, Golden Helix also offers on site training on HelixTree. The on-site training is very beneficial for teams of people. Contact our sales staff to discuss your on site training options.
We are always looking for ways to improve HelixTree both in its basic capabilities as well as in its ability to inter-operate
with other tools used in your work. HelixTree now has a feedback mechanism which is intended to encourage you to
communicate feature requests, bugs(!), as well as your experiences with the product.
We look forward to hearing from you.
Christophe Lambert
President & CEO of Golden Helix
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
II Recursive Partitioning
7 Interactive Tree Analysis
7.1 Tree Analysis Overview
7.2 Setting Options for Tree Analysis
7.3 Working with Nodes
7.4 Manually Splitting Nodes
7.5 Defining Splits
7.6 The File Menu
7.7 The Tree Menu
7.8 The Font Menu - Resizing and Formatting Tree View
8 Prediction Recipes
8.1 Training and Validation Recipe
8.2 Predicting An Unknown Response
9 Random Tree Generation
9.1 Random Tree Overview
9.2 Creating a Random Tree Model
9.3 Multitree Model Browsing - Tree View
10 Multivariate Tree Analysis
10.1 Multivariate Analysis Overview
10.2 Using More Than One Dependent Variable
11 Histogram Node Analysis
11.1 Histogram Overview
11.2 Viewing Split Data Histograms
12 The Observation Distance Matrix
12.1 Observation Distance Matrix Overview
12.2 Viewing Observation Distance Matrix
12.3 Printing and Saving the Observation Distance Matrix
13 The Correlation Interaction View
13.1 Correlation Interaction Overview
13.2 Viewing Correlation Interactions
14 Linkage Disequilibrium View
14.1 Linkage Disequilibrium Overview
14.2 Plotting Linkage Disequilibrium
14.3 The File Menu
14.4 LD Computation
15 Hardy Weinberg Equilibrium View
15.1 Plotting Hardy Weinberg
16 P-Value and Spreadsheet Plots
16.1 Plotting P-Values and Spreadsheet Columns
16.2 P-Value Plot Types
16.3 Plot Functions
16.4 The File Menu
17 Haplotype Regression and the Allele Table
17.1 Plotting Haplotype Regression
17.2 Displaying the Allele Table
18 Genetic Association Tests
18.1 Genetic Association Tests Overview
18.2 Genetic Models and Other Genetic Tests
18.3 Test Statistics
18.4 Missing Values
18.5 Multiple Testing Corrections
18.6 Correction for Stratification
18.7 Overall Marker Statistics
18.8 Using the Association Test Window
18.9 Using the Separate Principal Components Analysis Window
18.10 Using the Separate General Marker Statistics Window
19 EM Haplotype Frequency Estimation
19.1 Haplotype Frequency Estimation Overview
19.2 Window Display and Navigation
19.3 Example of Using the Patient List
19.4 EM Table and CHM Table
19.5 The Diplotype Table
20 Two-Loci Genetic Plot
20.1 Two-Loci Genetic Plot Overview
21 Runs of Homozygosity
21.1 Runs of Homozygosity Overview
21.2 Using Runs of Homozygosity
21.3 The ROH Algorithm
22 Text Viewer
22.1 Text Viewer Overview
22.2 Navigating the Text Viewer Menus
23 PBAT Family-Based Analysis (Optional Module)
23.1 PBAT Family-Based Analysis Overview
23.2 Using PBAT Capabilities through HelixTree
23.3 PBAT Power Calculations
23.4 PBAT Data Analysis
23.5 PBAT Data Analysis for Copy Number Variation
23.6 A Glossary of Terms Used in Family-Based Analysis
24 Regression Analysis (Optional Module)
24.1 Regression Analysis Overview
24.2 Performing Analysis
25 Copy Number Analysis (Optional Module)
25.1 Copy Number Analysis Overview
25.2 Preparing the Log2 Ratio Data
25.3 Using the Copy Number Analysis Segmentation Tool
25.4 Outputs of the Copy Number Analysis Segmentation Tool
25.5 Import LogR DSF Values Directly
25.6 Save LogR DSF Values as CNT Files
25.7 Using the LogR Association Tests and PCA Window
25.8 Visualizing Copy Number Analysis Results
25.9 Copy Number Analysis Examples and Tutorials
25.10 Golden Helix Copy Number Segmentation Algorithm
25.11 Workflow for Reading Affymetrix CEL Files
III The Science Behind HelixTree
26 Formulas and Theories
26.1 Split-Prediction Methodology
26.2 Normally Distributed Response Binomial Predictor
26.3 Normally Distributed Response Continuous-Ordinal Predictor
26.4 Normally Distributed Response Categorical Predictor
26.5 Linear Regression From a Tree Node
26.6 Haplotype Trend Regression (HTR) with Continuous Response
26.7 Composite Haplotype Method (CHM)
26.8 Haplotype Trend Regression (HTR) with Continuous Response and Covariates (Optional Module)
26.9 Stepwise Regression (Optional Module)
26.10 Categorical Covariates and Interaction Terms (Optional Module)
26.11 Results from Linear Regression (Optional Module)
26.12 Binomially Distributed Response Binary Predictor
26.13 Binomially Distributed Response Continuous/Ordinal Predictor
26.14 Binomially Distributed Response Categorical Predictor
26.15 Logistic Regression From a Tree Node
26.16 Haplotype Trend Regression (HTR) with Binomial Response
26.17 Haplotype Trend Regression (HTR) with Binomial Response and Covariates (Optional Module)
26.18 Results from Logistic Regression (Optional Module)
26.19 Categorical Response
26.20 The False Discovery Rate and the Simes Method
26.21 Permutation Test Methodology
26.22 Methods for the Genetic Association Tests
26.23 Formulas for Principal Components Analysis
26.24 Methods for Obtaining General Marker Statistics
A EULA
B Installing the Third-Party Condor
Package
B.1 Installing Condor
Overview
B.2 Downloading and Using the Installation Wizard
B.3 Troubleshooting Techniques and Common Issues
C Extracting Affymetrix Copy Number Data for use in HelixTree
C.1 Extracting Affymetrix Copy Number Data Overview
C.2 Creating CNT Files using the Affymetrix CNAT Batch Analysis Tool
C.3 Creating CNCHP Files using Affymetrix Genotyping Console 2.0
C.4 Affymetrix CNT File Format
D Exporting Data from BeadStudio
D.1 Exporting Data From BeadStudio Overview
D.2 Exporting Genotype Data using the BeadStudio Final Report
D.3 Exporting Copy Number Data using the HelixTree DSF Plug-In
E Platform Notes
E.1 Microsoft Windows
E.2 Linux
E.3 Mac OS X
F Bug Fix History
F.1 Bugs Fixed by Version
G Bibliography
Bibliography