Contents
I Installing HelixTree and Acquiring Data
1 Installing and Initializing HelixTree
1.1 Installation Overview
1.1.1 Installation Under Windows
1.1.2 Installation Under Apple
1.1.3 Installation Under Linux
1.1.4 Software Registration and Activation
1.1.4.1 Manually Setting Proxy Settings
1.1.4.2 Adding Personal Information
1.1.5 Alternate Software Activation via Email
1.2 Release Notes
1.2.1 Improvements in version 6.4
1.2.2 Improvements in version 6.3
1.2.3 Improvements in version 6.2
1.2.4 Improvements in version 6.1
1.2.5 Bug Fixes
1.2.6 Known Bugs
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
2.4.1 Create a New Project
2.4.2 Import A Data Set
2.4.3 View Imported Data in a Spreadsheet Viewer
2.4.4 Identify the Data Columns to be Used in Analysis
2.4.5 Perform the Analysis
2.4.6 Export Analysis Results for Publishing
2.5 Tutorial 2: Performing the Basic Workflow in Scripting Mode
2.5.1 Scripting Language Basics
2.5.2 The Script Explained
2.5.3 Executing the Script
2.5.4 Comparing the Results
2.6 Tutorial 3: Detailed Guide to a Standard Case/Control Association Study
2.6.1 Association Demo Overview
2.6.2 Discussion of Case/Control Association Studies
2.6.3 SNP Selection
2.6.4 First Stage of Genotyping
2.6.4.1 Importing Your Data
2.6.4.2 Checking For Deviation from HWE
2.6.4.3 Calculating Pairwise LD
2.6.4.4 Estimating Haplotype Frequencies
2.6.5 Characterizing htSNPs
2.6.6 Second Stage of Genotyping
2.6.7 Looking for Associations with Disease
2.6.7.1 Finding Single-Point Associations
2.6.7.2 Compare Haplotype Frequencies
3 Navigating the Main Screen
3.1 Main Screen Overview
3.1.1 The Menu Bar
3.1.2 New Project
3.2 Project Viewer Window
3.2.1 The Menu Bar
3.2.2 The Tool Bar
3.2.3 The Project Navigator Window
3.2.4 The Node Change Log Window
3.2.5 The Edit Annotations Window
3.3 Navigator Nodes
3.3.1 Viewer Windows
3.3.2 Types of Navigator Nodes and Their Associated Viewers
3.3.2.1 The Project Node
3.3.2.2 The Dataset Node
3.3.2.3 The Spreadsheet Node
3.3.2.4 Tree Analysis Node
3.3.2.5 Multitree Model Node
3.3.2.6 Applied Tree Node
3.3.2.7 Histogram Node
3.3.2.8 Observation Distance Matrix Node
3.3.2.9 Correlation Interaction Node
3.3.2.10 Linkage Disequilibrium Node
3.3.2.11 Two-Loci Node
3.3.2.12 Hardy Weinberg Equilibrium Node
3.3.2.13 Carlson SNP Tags Node
3.3.2.14 P Value Node
3.3.2.15 Text Node
3.3.2.16 Distributed Progress Node
3.4 The File Menu
3.4.1 Open Project
3.4.2 Save Project
3.4.3 Close Project
3.4.4 Recent Project Files
3.4.5 Import Data
3.4.6 Quit
3.5 The Tools Menu
3.5.1 Options for Updates and New Projects
3.5.2 Current Project’s Options
3.5.3 Project Option Settings Available
3.5.3.1 Tree Options
3.5.3.2 Node View Options
3.5.3.3 LD Parms
3.5.3.4 Appearance
3.5.3.5 Other
3.5.4 View Project Log - Sorted by Node
3.5.5 View Project Log - Chronological
3.5.6 Run Script
3.5.7 Download Affymetrix Library Files
3.5.8 Run Python Shell
3.5.9 Update HelixTree
3.6 The CNAM Menu
3.7 The PBAT Menu
3.7.1 Family Based Data Import
3.7.1.1 Running PBAT CNV Analysis
3.7.2 PBAT Power Calculations
3.8 The Help Menu
4 Importing Your Data Into HelixTree
4.1 General Considerations
4.2 Mathematical Considerations
4.2.1 P-Values and Dependent Variables
4.2.2 Regression and Independent Variables
4.2.3 P-Value Algorithms
4.2.4 Preparing Data Example
4.3 Importing Data
4.3.1 The Import Wizard
4.3.1.1 Importing Files
4.3.1.2 Importing ODBC Data
4.3.2 Importing ASCII Data Files
4.3.3 Importing Legacy GHD Files
4.3.4 Importing DSF Files
4.3.5 Importing Genetic Marker Maps
4.3.5.1 Importing Genetic Marker Maps Overview
4.3.5.2 Importing A Genetic Marker Map
4.3.5.3 Importing a Genetic Marker Map Using Affymetrix NetAffx
4.3.5.4 Associating A Genetic Marker Map with a Data File
4.3.6 Importing Affymetrix CHP files
4.3.6.1 Affymetrix Files Installation
4.3.6.2 Affymetrix Mapping Array Import
4.3.7 Import PED/BED File
4.3.7.1 Text PED/MAP File Import
4.3.7.2 Binary BED/FAM/BIM File Import
4.3.8 Downloading Affymetrix Library Files Using the NetAffx Service
4.4 Importing Copy Number Data
4.4.1 Import Affymetrix Data
4.4.1.1 Import CEL Files
4.4.1.2 Import CNT Files
4.4.1.3 Import CNCHP Files
4.4.2 Import Illumina Data
4.4.3 Appending DSF Files
4.4.4 Directly Import LogR Data
4.4.5 Run Copy Number Segmentation
4.5 Importing Family-Based Data
4.5.1 Preparing Family Data
4.5.2 Importing Family Data
5 Scripting and Other Integrated Statistical Tools
5.1 Integrated Tools Overview
5.2 The Python Shell Window
5.2.1 Using Shell Objects
5.2.2 Using the Dir Command
5.2.3 Using Python for Getting Help
5.3 Running Scripts
5.3.1 Command Line Invocation
5.3.2 Python Shell Invocation
5.3.3 Navigator Menu Invocation
5.3.4 Script Server Invocation
5.4 Selecting a Script Server
5.5 Example Scripts
5.6 Scripting Reference
5.6.1 Project Related Commands
5.6.1.1 Creating a New Project
5.6.1.2 Creating a Temporary Project
5.6.1.3 Open an Existing Project
5.6.1.4 Saving a Project
5.6.1.5 Closing a Project
5.6.2 General GHI Commands
5.6.2.1 Allowing Viewers to Display
5.6.2.2 Allowing Log Messages to Be Created
5.6.2.3 Display a GUI Message
5.6.2.4 Display a GUI Error Message
5.6.2.5 Getting a Specific Navigator Node
5.6.2.6 Getting the Current Navigator Node
5.6.2.7 Choosing a File
5.6.2.8 Choosing a Directory
5.6.2.9 Creating a Progress Bar
5.6.2.10 Setting the Progress Bar’s Progress
5.6.2.11 Checking if the Progress Bar Has Been Cancelled
5.6.2.12 Disposing of a Progress Bar When Done
5.6.2.13 Creating a Status Dialog
5.6.2.14 Setting the Status Dialog’s Message
5.6.2.15 Closing the Status Dialog When Done
5.6.3 Commands Common to All Objects
5.6.3.1 Change a Navigator Node Name
5.6.3.2 Getting a Navigator Node Name
5.6.3.3 Getting a Navigator Node Type
5.6.3.4 Getting a Navigator Node ID
5.6.3.5 Deleting a Navigator Node
5.6.3.6 Closing a Navigator Viewer
5.6.3.7 Showing a Navigator Viewer
5.6.3.8 Finding a Node’s Parent
5.6.3.9 Finding a Node’s Secondary Parent
5.6.3.10 Getting a Node’s Annotations
5.6.3.11 Appending to a Node’s Annotations
5.6.4 Importing and Loading Data
5.6.4.1 Importing GHD-format Data Sets
5.6.4.2 Importing DSF Files
5.6.4.3 Importing Various File Formats
5.6.4.4 Importing ASCII files
5.6.4.5 Importing Family-Indexed Data
5.6.4.6 Importing PED files
5.6.4.7 Importing BED files
5.6.4.8 Extracting Copy Number Values From Affymetrix CEL Files
5.6.4.9 Importing a Marker Map File
5.6.5 Creating a New Data Set with Scripting
5.6.5.1 Getting a Dataset Builder Object
5.6.5.2 Adding Row Labels
5.6.5.3 Adding a Column of Boolean Values
5.6.5.4 Adding a Column of Integer Values
5.6.5.5 Adding a Column of Double Values
5.6.5.6 Adding a Column of Nominal Values
5.6.5.7 Adding a Column of Genetic Values
5.6.5.8 Creating the Data Set
5.6.6 Spreadsheet Access and Manipulation
5.6.6.1 Getting the Spreadsheet as a Dictionary
5.6.6.2 Getting the Spreadsheet as a List of Lists
5.6.6.3 Getting a Spreadsheet Cell
5.6.6.4 Getting a Spreadsheet Column by Column Number
5.6.6.5 Getting a Spreadsheet Column by Column Name
5.6.6.6 Determining if a Spreadsheet is a Marker Map
5.6.6.7 Get a Spreadsheet Column Type
5.6.6.8 Get a Spreadsheet Column State
5.6.6.9 Selecting Columns by Chromosome, Region, or Gene Ranges
5.6.6.10 Obtain Marker Map Information from a Spreadsheet
5.6.6.11 Export a Spreadsheet to CSV File
5.6.6.12 Export a Spreadsheet to a DSF File
5.6.6.13 Export a Spreadsheet to FBAT Pedigree File
5.6.6.14 Export a Spreadsheet to FBAT Phenotype File
5.6.6.15 Export a Spreadsheet PED/MAP File
5.6.6.16 Finding a Column by Name
5.6.6.17 Finding a Row by Name
5.6.6.18 Invert Row States
5.6.6.19 Getting the Number of Spreadsheet Columns
5.6.6.20 Get the Number of Columns in a State
5.6.6.21 Get the Number of Spreadsheet Rows
5.6.6.22 Get the Number of Rows in a State
5.6.6.23 Randomly Shuffle Rows
5.6.6.24 Getting a Row of Data
5.6.6.25 Change the State of a Single Column
5.6.6.26 Change the State of a Range of Columns
5.6.6.27 Setting the State of a Single Row
5.6.6.28 Getting the State of a Single Row
5.6.6.29 Setting the State of a Range of Rows
5.6.6.30 Setting the State of a Defined Set of Rows
5.6.6.31 Randomly set a Number of Rows to a State
5.6.6.32 Randomly Set a Percentage of Rows to a State
5.6.6.33 Sort a Column in Ascending Order
5.6.6.34 Sort a Column in Descending Order
5.6.6.35 Remove Column Sorting
5.6.6.36 Remembering a Spreadsheet Page
5.6.6.37 Joining Two Spreadsheets
5.6.6.38 Creating a Linkage Disequilibrium Plot
5.6.6.39 Creating Hardy-Weinberg Plots
5.6.6.40 Creating Two-Loci Genetic Plots
5.6.6.41 Creating an Allele Test Plot
5.6.6.42 Plotting Numeric Spreadsheet Columns
5.6.6.43 Plotting a Spreadsheet Column
5.6.6.44 Performing Genetic Association Tests
5.6.6.45 Finding Runs of Homozygosity
5.6.6.46 Inferring Missing Values
5.6.6.47 Creating Haplotype Frequency Tables
5.6.6.48 Applying a Marker Map
5.6.7 Using the Linkage Disequilibrium Object
5.6.7.1 Getting All LD Values in a Dictionary
5.6.7.2 Getting R Squared for Specified Markers
5.6.7.3 Getting D Prime for Specified Markers
5.6.7.4 Getting Neg Log10 P for Specified Markers
5.6.7.5 Getting Chi Squared for Specified Markers
5.6.7.6 Getting P Value for Specified Markers
5.6.7.7 Getting Carlson SNP Tags
5.6.8 Using the Hardy Weinberg Object
5.6.8.1 Getting All HWE Values in a Dictionary
5.6.8.2 Getting Neg Log10 P for a Marker
5.6.8.3 Getting R Squared for a Marker
5.6.8.4 Getting P Value for a Marker
5.6.8.5 Getting Chi Squared for a Marker
5.6.9 Using the Two-Loci Object
5.6.9.1 Getting All Two-Loci P-Values in a Dictionary
5.6.9.2 Getting P for Two Markers
5.6.9.3 Getting Adjusted P for Two Markers
5.6.9.4 Getting Bonferonni P for Two Markers
5.6.9.5 Getting Neg Log10 of All Two-Loci P Values in a Dictionary
5.6.9.6 Getting Neg Log10 P for Two Markers
5.6.9.7 Getting Neg Log10 Adjusted P for Two Markers
5.6.9.8 Getting Neg Log10 Bonferonni P for Two Markers
5.6.9.9 Getting Detailed Split Information for Two Markers
5.6.10 Using the P-Value plot
5.6.10.1 Getting P-Values
5.6.10.2 Getting Simes P-Values
5.6.10.3 Setting the Simes Window
5.6.10.4 Getting FDR (aP)
5.6.10.5 Getting all P-Values as a Spreadsheet
5.6.10.6 Getting an Allele Frequency Spreadsheet for a Specific Column
5.6.11 Getting and Setting Tree Options
5.6.11.1 Setting the Minimum Elements for Splitting
5.6.11.2 Setting the Number of Threads
5.6.11.3 Setting the P Value Threshold
5.6.11.4 Setting the Pairwise Threshold
5.6.11.5 Setting the P Threshold Type
5.6.11.6 Setting the Minimum Haplotype Frequency
5.6.11.7 Setting the Haplotype Estimation Method
5.6.11.8 Setting the Segmenting Algorithm
5.6.11.9 Setting the Maximum Segments
5.6.11.10 Setting Resample Iterations
5.6.11.11 Setting Linear Regression
5.6.11.12 Setting Use Missing Values Option
5.6.11.13 Setting Non-Genetic Splits
5.6.11.14 Setting Genotype Splits
5.6.11.15 Setting Haplotype Splits
5.6.12 Creating a Tree Model
5.6.13 Importing a Legacy Tree Model
5.6.14 Tree Model Commands
5.6.14.1 Get Variable Frequencies
5.6.14.2 Get Tree Predictions
5.6.14.3 Get Tree Variables
5.6.14.4 Get Correlation Table
5.6.14.5 Get Correlation Plot
5.6.14.6 Get Observation Distance Matrix Unsorted
5.6.14.7 Get Observation Distance Matrix Sorted by First Principal Component
5.6.14.8 Get Observation Distance Sorted by Similarity to One Observation
5.6.15 Using the Distance Matrix Object
5.6.15.1 Get the Observation Label for a Distance Matrix Plot
5.6.15.2 Get the Observation Number for a Distance Matrix Plot
5.6.15.3 Get the Rank Index for a Distance Matrix Plot
5.6.15.4 Get the Distance Values by Row Number for a Distance Matrix Plot
5.6.15.5 Get the Distance Values by Rank Index for a Distance Matrix Plot
5.6.16 Applying a Tree Model
5.6.17 Copy Number Analysis
5.6.18 Importing Raw Copy Number Values
5.6.19 Performing LogR Association Tests and PCA
5.6.20 Performing Regression
5.6.21 Output a C File
5.6.22 Prompting the User for Input
5.6.23 Text Viewer
5.6.23.1 Getting the text
5.6.23.2 Saving text to a file
5.6.24 Regression Results
5.6.24.1 Getting the text
5.6.24.2 Saving text to a file
5.6.24.3 Getting the covariates
5.6.24.4 Getting the markers
5.6.24.5 Getting the interactions
5.6.25 Navigator Object Selection
5.6.25.1 Selecting a Spreadsheet
5.6.25.2 Selecting a Tree model
5.7 S-PLUS Integration
5.7.1 S-PLUS Desktop Integration
5.7.2 S-PLUS Client/Server 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
6.2.1 Dependent or Independent Variable?
6.2.2 Selecting a Dependent
6.2.3 Deactivating Unwanted Columns
6.2.4 Sorting Records
6.2.5 Plotting Individual Columns
6.2.6 Activating - Deactivating Row Data
6.2.7 Picking Random Record Sets
6.3 The File Menu
6.3.1 Save As - Exporting Data
6.3.2 Save As Comma-Delimited Text File
6.3.3 Save As DSF File
6.3.4 Save As PED/MAP Files
6.3.5 Save Family Data
6.3.6 Apply Gene Marker Map
6.3.7 Join Spreadsheet on Row Labels
6.3.8 Join Spreadsheets With Uneven Row Numbers
6.3.9 Join family-indexed spreadsheets
6.3.10 Join Spreadsheets by Sorting
6.3.11 Import a Legacy Tree Model
6.3.12 Closing the File
6.4 The Edit Menu
6.4.1 Row
6.4.1.1 Activate All
6.4.1.2 Invert Selection
6.4.1.3 Select Subset
6.4.1.4 Subset Spreadsheet
6.4.2 Column
6.4.2.1 Activate All
6.4.2.2 Inactivate All
6.4.2.3 Invert Selection
6.4.2.4 Select Columns by Chromosome/Region Range
6.4.2.5 Find
6.4.2.6 Subset Spreadsheet
6.5 The Analysis Menu
6.5.1 Interactive Tree Analysis
6.5.2 Create a Multiple-Tree Model
6.5.3 Apply a Tree Model
6.5.4 Regression Analysis
6.5.5 Plot Numeric Columns
6.6 The Genetics Menu
6.6.1 Genetic Association Tests
6.6.2 Marker Statistics
6.6.3 Principal Component Analysis
6.6.4 EM Haplotype Frequency Estimation
6.6.5 HWE Plot
6.6.6 LD Plot
6.6.7 PBAT Family-Based Analysis
6.6.8 Runs of Homozygosity
6.6.9 Infer Missing Genotypes
6.7 The Help Menu
II Recursive Partitioning
7 Interactive Tree Analysis
7.1 Tree Analysis Overview
7.2 Setting Options for Tree Analysis
7.2.1 The Tree Tab
7.2.1.1 Minimum Elements per Child:
7.2.1.2 Segmenting Algorithm:
7.2.1.3 Max Segments:
7.2.1.4 Parallel Threads:
7.2.1.5 Resampling Iterations
7.2.1.6 P Value Threshold:
7.2.1.7 Use Missing Values as Predictors (Impute Missing Data for HTR)
7.2.1.8 Linear/Logistic Regression:
7.2.1.9 Non-Genetic Splits
7.2.1.10 Genotype Split
7.2.1.11 Haplotype Trend Regression
7.2.1.12 Fixed Window Size
7.2.1.13 Ignore Marker Mapping
7.2.1.14 Window Size Using Genetic Distance of ____ Units
7.2.1.15 Marker Window Size
7.2.1.16 Minimum Frequency
7.2.1.17 Estimate Frequencies Using CHM or EM
7.2.2 The Node View Tab
7.2.2.1 What the Node Values Mean
7.2.3 The Linkage Disequilibrium Parameters Tab
7.2.3.1 Linkage Disequilibrium CHM vs. EM
7.2.3.2 Hardy Weinberg Correction when Both Markers are Biallelic
7.2.3.3 Use Patient Data Containing Missing Values
7.2.3.4 Maximum EM Iterations
7.2.3.5 EM Convergence Tolerance
7.3 Working with Nodes
7.3.1 Node Pop-up Menu Selections
7.3.1.1 Split Node
7.3.1.2 Manual Split
7.3.1.3 Collapse/Expand
7.3.1.4 Recursive Split
7.3.1.5 Spreadsheet
7.3.1.6 Resample
7.3.1.7 Visualize Genetics
7.3.2 Visualize Split Data
7.3.3 Visualize Split Data->Multiple Tree Clustering
7.3.4 Visualize Split Data->Histogram
7.3.5 Showing Split Data
7.3.5.1 Linear Regression Splits
7.3.5.2 Logistic Regression Splits
7.3.5.3 Splits on Continuous Predictors
7.3.5.4 Splits on Categorical Predictors
7.4 Manually Splitting Nodes
7.4.1 P Value Plots
7.4.2 Define Split
7.4.3 Don’t Split
7.4.4 Manual Split with Regression
7.4.5 Using the Tree and Manual Split Window Together
7.5 Defining Splits
7.5.1 The Split Point
7.5.2 The Split Point Controls the Node Information
7.5.3 Smoothing the Data Points
7.5.4 Refined or Course Data Points
7.5.5 Zooming into a Specific Region
7.5.6 Adding Linear Regression
7.5.7 Categorical Predictors
7.6 The File Menu
7.6.1 File->Print tree
7.6.2 File->Save Tree Image
7.6.3 File->View Predictions (In-Sample)
7.6.4 File->Output C Code
7.6.5 File->Close
7.7 The Tree Menu
7.7.1 Tree->Options
7.7.2 Tree->Subset Spreadsheet
7.7.3 Tree->Subset Tree
7.7.4 Tree->Extend Current Tree Randomly
7.7.5 Tree->Search Tree
7.7.5.1 Tree->SearchTree->Find Observation
7.7.5.2 Tree->SearchTree->Find Node
7.7.5.3 Tree->SearchTree->Select Node by Threshold
7.7.5.4 Tree->SearchTree->Highlight All Nodes
7.7.5.5 Tree->SearchTree->UnHighlight All Nodes
7.8 The Font Menu - Resizing and Formatting Tree View
7.8.1 Font->Size
7.8.2 Font->Family
8 Prediction Recipes
8.1 Training and Validation Recipe
8.2 Predicting An Unknown Response
8.2.1 Modifying a Copy of Data
8.2.2 Converting to a GHD File
8.2.3 Create a Subset With BP Readings
8.2.4 Create Random Trees From Initial Dataset
8.2.5 Invert Data to Create Dataset With Missing BP
8.2.6 Applying A Multitree Model To Make Predictions
9 Random Tree Generation
9.1 Random Tree Overview
9.2 Creating a Random Tree Model
9.3 Multitree Model Browsing - Tree View
9.3.1 Multitree Model – Tree List
9.3.2 Multitree Model – Variable List
9.3.2.1 Sorting
9.3.2.2 Subset
9.3.2.3 Variables->View Variable Usage
9.3.2.4 Variables->View Variable Frequency
9.3.2.5 Viewing Variable Correlations
9.3.3 File->Analyze Current Tree Tools
9.3.4 Predictions (InSample)->View Average Tree In-Sample Predictions
9.3.5 Predictions (InSample)->Save All Tree In-Sample Predictions to CSV File
9.3.6 Save “C” Prediction Program
9.3.7 Close
9.3.8 Help
10 Multivariate Tree Analysis
10.1 Multivariate Analysis Overview
10.2 Using More Than One Dependent Variable
10.2.1 Continuous Multivariate Response
10.2.2 Binary and/or Categorical Multivariate Response
10.2.3 Multivariate Multiple Tree Clustering
10.2.4 File->Output C Code
11 Histogram Node Analysis
11.1 Histogram Overview
11.2 Viewing Split Data Histograms
11.2.1 Creating Histograms
11.2.2 Visualizing Node Relationships
11.2.3 Changing Bins
11.2.4 Zooming or Rubber Banding Data
11.2.5 Menus
11.2.6 File->Print
12 The Observation Distance Matrix
12.1 Observation Distance Matrix Overview
12.1.1 Creating an Observation Distance Matrix
12.1.2 The Observation Distance Matrix
12.1.3 Set Axes
12.1.4 Stop Calculation/Stop Refresh and Restore Calculation/Restore Refresh
12.1.5 Copy to Clipboard
12.1.6 Creating a Spreadsheet or Tree view from the Matrix Plot
12.1.7 Zoom Mode
12.1.8 Modify Color Scaling
12.1.9 Effect of Clicking on the Plot
12.1.10 Color Drop Down Menu
12.2 Viewing Observation Distance Matrix
12.2.1 Viewing Spreadsheets or Trees of Subsets
12.2.2 Zooming-In on a Subset of the Distance Matrix Plot
12.2.3 Narrowing the Distance Range
12.2.4 Menus
12.3 Printing and Saving the Observation Distance Matrix
12.3.1 Save Image or Print
12.3.2 The Menus
12.3.3 File->Save Obs. Distance Matrix (Sorted)
13 The Correlation Interaction View
13.1 Correlation Interaction Overview
13.1.1 Pick Wanted Variables
13.2 Viewing Correlation Interactions
13.2.1 The Correlation Interaction View
13.2.2 The Upper Triangle
13.2.3 The Lower Triangle
14 Linkage Disequilibrium View
14.1 Linkage Disequilibrium Overview
14.2 Plotting Linkage Disequilibrium
14.2.1 Stop Calculation/Stop Refresh and Resume Calculation/Resume Refresh
14.2.2 Copy to Clipboard
14.2.3 Plot Visual: Color or Black and White
14.2.4 Fill Mode
14.2.5 Zoom Mode
14.2.6 Click on Graph
14.2.7 Modify Color Scaling
14.3 The File Menu
14.3.1 Create Bitmap
14.3.2 Print Image
14.3.3 Summarize Data for All Points to CSV File
14.3.4 Output Genotypes for Current Point to CSV File
14.3.5 Output Genotype Combinations for Current Point
14.3.6 Output Allele Counts for Current Point
14.3.7 Output Allele Combinations for Current Point
14.3.8 View Carlson-Method SNP Tags
14.4 LD Computation
14.4.1 LD Computation for D prime
14.4.2 LD Computation for Quick Mode
15 Hardy Weinberg Equilibrium View
15.1 Plotting Hardy Weinberg
15.1.1 Hardy Weinberg Equilibrium Plot
15.1.2 Reset View
15.1.3 Copy to Clipboard
15.1.4 Axis Selector
15.1.5 Zooming into the Graph
15.1.6 File Menu
15.1.7 Create Bitmap
15.1.8 Print Image
15.1.9 Summarize All Data to CSV File
15.1.10 Output All Allele Tables to CSV File
15.1.11 Output All Genotype Tables to CSV File
15.1.12 Hardy-Weinberg Equilibrium computation
16 P-Value and Spreadsheet Plots
16.1 Plotting P-Values and Spreadsheet Columns
16.2 P-Value Plot Types
16.2.1 P-Values Sorted by Var # from the Manual Split Window
16.2.2 FDR and P-Values from the Manual Split Window
16.2.3 P-Values Resulting from Regression Analysis Using a Moving Window
16.2.4 Spreadsheet Column Plots
16.3 Plot Functions
16.3.1 Clicking at a Point to Show Values
16.3.2 Reset View
16.3.3 Copy to Clipboard
16.3.4 View Regression Results (Regression Plots Only)
16.3.5 Axis Selector
16.3.6 Logarithm Mode Selector (Spreadsheet Plots Only)
16.3.7 Zooming into the Graph
16.4 The File Menu
16.4.1 Create Bitmap
16.4.2 Print Image
16.4.3 P-Value Spreadsheet
17 Haplotype Regression and the Allele Table
17.1 Plotting Haplotype Regression
17.1.1 Haplotype Regression
17.1.2 Obtaining a Haplotype Regression
17.1.3 Viewing the Details of the Regression
17.1.4 Residual Spreadsheet
17.1.5 Regression Statistics
17.1.5.1 Overall Statistics
17.1.5.2 Regressor Statistics
17.1.5.3 Left-Out Regressors
17.1.5.4 Table of Haplotypes
17.1.5.5 Parameters
17.2 Displaying the Allele Table
17.2.0.6 Display Allele Table
18 Genetic Association Tests
18.1 Genetic Association Tests Overview
18.2 Genetic Models and Other Genetic Tests
18.2.1 Basic Allelic Tests
18.2.2 Genotypic Tests
18.2.3 Additive Model
18.2.4 Dominant Model
18.2.5 Recessive Model
18.3 Test Statistics
18.3.1 Correlation/Trend Test
18.3.2 Armitage Trend Test
18.3.3 Exact Form of Armitage Test
18.3.4 (Pearson) Chi-Squared Test
18.3.5 Fisher’s Exact Test
18.3.6 Odds Ratio with Confidence Limits
18.3.7 Analysis of Deviance
18.3.8 F-Test
18.4 Missing Values
18.4.1 Using Missing Values for Genotypes
18.4.2 Missing Values in a Case/Control Variable
18.5 Multiple Testing Corrections
18.5.1 Bonferonni Adjustment
18.5.2 False Discovery Rate
18.5.3 Permutation Testing
18.5.3.1 Single Value Permutation Testing
18.5.3.2 Full Scan Permutation Testing
18.6 Correction for Stratification
18.6.1 Correction of Input Data by Principal Components Analysis
18.6.2 Working Premise
18.6.3 The PCA Technique
18.6.4 How Many Components to Use?
18.6.5 A Second Answer
18.6.6 Removing Outlier Subjects
18.6.7 PCA-Corrected Association Testing
18.6.8 Correction of Output Chi-Square Values and P-Values by Genomic Control
18.7 Overall Marker Statistics
18.7.1 Minor Allele Frequency
18.7.2 Output Spreadsheet of DD/Dd/dd genotypes
18.7.3 Call Rate
18.7.4 Hardy-Weinberg Equilibrium P-Value
18.7.5 Fisher’s Exact Test for HWE P-Value
18.7.6 Signed HWE R
18.7.7 Genotype Count Table(s)
18.7.8 Allele Count Table(s)
18.8 Using the Association Test Window
18.8.1 Data Requirements
18.8.2 Available Tabs
18.8.3 The Association Test Parameters Tab
18.8.4 Principal Component Analysis Parameters Tab
1 Installing and Initializing HelixTree
1.1 Installation Overview
1.1.1 Installation Under Windows
1.1.2 Installation Under Apple
1.1.3 Installation Under Linux
1.1.4 Software Registration and Activation
1.1.4.1 Manually Setting Proxy Settings
1.1.4.2 Adding Personal Information
1.1.5 Alternate Software Activation via Email
1.2 Release Notes
1.2.1 Improvements in version 6.4
1.2.2 Improvements in version 6.3
1.2.3 Improvements in version 6.2
1.2.4 Improvements in version 6.1
1.2.5 Bug Fixes
1.2.6 Known Bugs
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
2.4.1 Create a New Project
2.4.2 Import A Data Set
2.4.3 View Imported Data in a Spreadsheet Viewer
2.4.4 Identify the Data Columns to be Used in Analysis
2.4.5 Perform the Analysis
2.4.6 Export Analysis Results for Publishing
2.5 Tutorial 2: Performing the Basic Workflow in Scripting Mode
2.5.1 Scripting Language Basics
2.5.2 The Script Explained
2.5.3 Executing the Script
2.5.4 Comparing the Results
2.6 Tutorial 3: Detailed Guide to a Standard Case/Control Association Study
2.6.1 Association Demo Overview
2.6.2 Discussion of Case/Control Association Studies
2.6.3 SNP Selection
2.6.4 First Stage of Genotyping
2.6.4.1 Importing Your Data
2.6.4.2 Checking For Deviation from HWE
2.6.4.3 Calculating Pairwise LD
2.6.4.4 Estimating Haplotype Frequencies
2.6.5 Characterizing htSNPs
2.6.6 Second Stage of Genotyping
2.6.7 Looking for Associations with Disease
2.6.7.1 Finding Single-Point Associations
2.6.7.2 Compare Haplotype Frequencies
3 Navigating the Main Screen
3.1 Main Screen Overview
3.1.1 The Menu Bar
3.1.2 New Project
3.2 Project Viewer Window
3.2.1 The Menu Bar
3.2.2 The Tool Bar
3.2.3 The Project Navigator Window
3.2.4 The Node Change Log Window
3.2.5 The Edit Annotations Window
3.3 Navigator Nodes
3.3.1 Viewer Windows
3.3.2 Types of Navigator Nodes and Their Associated Viewers
3.3.2.1 The Project Node
3.3.2.2 The Dataset Node
3.3.2.3 The Spreadsheet Node
3.3.2.4 Tree Analysis Node
3.3.2.5 Multitree Model Node
3.3.2.6 Applied Tree Node
3.3.2.7 Histogram Node
3.3.2.8 Observation Distance Matrix Node
3.3.2.9 Correlation Interaction Node
3.3.2.10 Linkage Disequilibrium Node
3.3.2.11 Two-Loci Node
3.3.2.12 Hardy Weinberg Equilibrium Node
3.3.2.13 Carlson SNP Tags Node
3.3.2.14 P Value Node
3.3.2.15 Text Node
3.3.2.16 Distributed Progress Node
3.4 The File Menu
3.4.1 Open Project
3.4.2 Save Project
3.4.3 Close Project
3.4.4 Recent Project Files
3.4.5 Import Data
3.4.6 Quit
3.5 The Tools Menu
3.5.1 Options for Updates and New Projects
3.5.2 Current Project’s Options
3.5.3 Project Option Settings Available
3.5.3.1 Tree Options
3.5.3.2 Node View Options
3.5.3.3 LD Parms
3.5.3.4 Appearance
3.5.3.5 Other
3.5.4 View Project Log - Sorted by Node
3.5.5 View Project Log - Chronological
3.5.6 Run Script
3.5.7 Download Affymetrix Library Files
3.5.8 Run Python Shell
3.5.9 Update HelixTree
3.6 The CNAM Menu
3.7 The PBAT Menu
3.7.1 Family Based Data Import
3.7.1.1 Running PBAT CNV Analysis
3.7.2 PBAT Power Calculations
3.8 The Help Menu
4 Importing Your Data Into HelixTree
4.1 General Considerations
4.2 Mathematical Considerations
4.2.1 P-Values and Dependent Variables
4.2.2 Regression and Independent Variables
4.2.3 P-Value Algorithms
4.2.4 Preparing Data Example
4.3 Importing Data
4.3.1 The Import Wizard
4.3.1.1 Importing Files
4.3.1.2 Importing ODBC Data
4.3.2 Importing ASCII Data Files
4.3.3 Importing Legacy GHD Files
4.3.4 Importing DSF Files
4.3.5 Importing Genetic Marker Maps
4.3.5.1 Importing Genetic Marker Maps Overview
4.3.5.2 Importing A Genetic Marker Map
4.3.5.3 Importing a Genetic Marker Map Using Affymetrix NetAffx
4.3.5.4 Associating A Genetic Marker Map with a Data File
4.3.6 Importing Affymetrix CHP files
4.3.6.1 Affymetrix Files Installation
4.3.6.2 Affymetrix Mapping Array Import
4.3.7 Import PED/BED File
4.3.7.1 Text PED/MAP File Import
4.3.7.2 Binary BED/FAM/BIM File Import
4.3.8 Downloading Affymetrix Library Files Using the NetAffx Service
4.4 Importing Copy Number Data
4.4.1 Import Affymetrix Data
4.4.1.1 Import CEL Files
4.4.1.2 Import CNT Files
4.4.1.3 Import CNCHP Files
4.4.2 Import Illumina Data
4.4.3 Appending DSF Files
4.4.4 Directly Import LogR Data
4.4.5 Run Copy Number Segmentation
4.5 Importing Family-Based Data
4.5.1 Preparing Family Data
4.5.2 Importing Family Data
5 Scripting and Other Integrated Statistical Tools
5.1 Integrated Tools Overview
5.2 The Python Shell Window
5.2.1 Using Shell Objects
5.2.2 Using the Dir Command
5.2.3 Using Python for Getting Help
5.3 Running Scripts
5.3.1 Command Line Invocation
5.3.2 Python Shell Invocation
5.3.3 Navigator Menu Invocation
5.3.4 Script Server Invocation
5.4 Selecting a Script Server
5.5 Example Scripts
5.6 Scripting Reference
5.6.1 Project Related Commands
5.6.1.1 Creating a New Project
5.6.1.2 Creating a Temporary Project
5.6.1.3 Open an Existing Project
5.6.1.4 Saving a Project
5.6.1.5 Closing a Project
5.6.2 General GHI Commands
5.6.2.1 Allowing Viewers to Display
5.6.2.2 Allowing Log Messages to Be Created
5.6.2.3 Display a GUI Message
5.6.2.4 Display a GUI Error Message
5.6.2.5 Getting a Specific Navigator Node
5.6.2.6 Getting the Current Navigator Node
5.6.2.7 Choosing a File
5.6.2.8 Choosing a Directory
5.6.2.9 Creating a Progress Bar
5.6.2.10 Setting the Progress Bar’s Progress
5.6.2.11 Checking if the Progress Bar Has Been Cancelled
5.6.2.12 Disposing of a Progress Bar When Done
5.6.2.13 Creating a Status Dialog
5.6.2.14 Setting the Status Dialog’s Message
5.6.2.15 Closing the Status Dialog When Done
5.6.3 Commands Common to All Objects
5.6.3.1 Change a Navigator Node Name
5.6.3.2 Getting a Navigator Node Name
5.6.3.3 Getting a Navigator Node Type
5.6.3.4 Getting a Navigator Node ID
5.6.3.5 Deleting a Navigator Node
5.6.3.6 Closing a Navigator Viewer
5.6.3.7 Showing a Navigator Viewer
5.6.3.8 Finding a Node’s Parent
5.6.3.9 Finding a Node’s Secondary Parent
5.6.3.10 Getting a Node’s Annotations
5.6.3.11 Appending to a Node’s Annotations
5.6.4 Importing and Loading Data
5.6.4.1 Importing GHD-format Data Sets
5.6.4.2 Importing DSF Files
5.6.4.3 Importing Various File Formats
5.6.4.4 Importing ASCII files
5.6.4.5 Importing Family-Indexed Data
5.6.4.6 Importing PED files
5.6.4.7 Importing BED files
5.6.4.8 Extracting Copy Number Values From Affymetrix CEL Files
5.6.4.9 Importing a Marker Map File
5.6.5 Creating a New Data Set with Scripting
5.6.5.1 Getting a Dataset Builder Object
5.6.5.2 Adding Row Labels
5.6.5.3 Adding a Column of Boolean Values
5.6.5.4 Adding a Column of Integer Values
5.6.5.5 Adding a Column of Double Values
5.6.5.6 Adding a Column of Nominal Values
5.6.5.7 Adding a Column of Genetic Values
5.6.5.8 Creating the Data Set
5.6.6 Spreadsheet Access and Manipulation
5.6.6.1 Getting the Spreadsheet as a Dictionary
5.6.6.2 Getting the Spreadsheet as a List of Lists
5.6.6.3 Getting a Spreadsheet Cell
5.6.6.4 Getting a Spreadsheet Column by Column Number
5.6.6.5 Getting a Spreadsheet Column by Column Name
5.6.6.6 Determining if a Spreadsheet is a Marker Map
5.6.6.7 Get a Spreadsheet Column Type
5.6.6.8 Get a Spreadsheet Column State
5.6.6.9 Selecting Columns by Chromosome, Region, or Gene Ranges
5.6.6.10 Obtain Marker Map Information from a Spreadsheet
5.6.6.11 Export a Spreadsheet to CSV File
5.6.6.12 Export a Spreadsheet to a DSF File
5.6.6.13 Export a Spreadsheet to FBAT Pedigree File
5.6.6.14 Export a Spreadsheet to FBAT Phenotype File
5.6.6.15 Export a Spreadsheet PED/MAP File
5.6.6.16 Finding a Column by Name
5.6.6.17 Finding a Row by Name
5.6.6.18 Invert Row States
5.6.6.19 Getting the Number of Spreadsheet Columns
5.6.6.20 Get the Number of Columns in a State
5.6.6.21 Get the Number of Spreadsheet Rows
5.6.6.22 Get the Number of Rows in a State
5.6.6.23 Randomly Shuffle Rows
5.6.6.24 Getting a Row of Data
5.6.6.25 Change the State of a Single Column
5.6.6.26 Change the State of a Range of Columns
5.6.6.27 Setting the State of a Single Row
5.6.6.28 Getting the State of a Single Row
5.6.6.29 Setting the State of a Range of Rows
5.6.6.30 Setting the State of a Defined Set of Rows
5.6.6.31 Randomly set a Number of Rows to a State
5.6.6.32 Randomly Set a Percentage of Rows to a State
5.6.6.33 Sort a Column in Ascending Order
5.6.6.34 Sort a Column in Descending Order
5.6.6.35 Remove Column Sorting
5.6.6.36 Remembering a Spreadsheet Page
5.6.6.37 Joining Two Spreadsheets
5.6.6.38 Creating a Linkage Disequilibrium Plot
5.6.6.39 Creating Hardy-Weinberg Plots
5.6.6.40 Creating Two-Loci Genetic Plots
5.6.6.41 Creating an Allele Test Plot
5.6.6.42 Plotting Numeric Spreadsheet Columns
5.6.6.43 Plotting a Spreadsheet Column
5.6.6.44 Performing Genetic Association Tests
5.6.6.45 Finding Runs of Homozygosity
5.6.6.46 Inferring Missing Values
5.6.6.47 Creating Haplotype Frequency Tables
5.6.6.48 Applying a Marker Map
5.6.7 Using the Linkage Disequilibrium Object
5.6.7.1 Getting All LD Values in a Dictionary
5.6.7.2 Getting R Squared for Specified Markers
5.6.7.3 Getting D Prime for Specified Markers
5.6.7.4 Getting Neg Log10 P for Specified Markers
5.6.7.5 Getting Chi Squared for Specified Markers
5.6.7.6 Getting P Value for Specified Markers
5.6.7.7 Getting Carlson SNP Tags
5.6.8 Using the Hardy Weinberg Object
5.6.8.1 Getting All HWE Values in a Dictionary
5.6.8.2 Getting Neg Log10 P for a Marker
5.6.8.3 Getting R Squared for a Marker
5.6.8.4 Getting P Value for a Marker
5.6.8.5 Getting Chi Squared for a Marker
5.6.9 Using the Two-Loci Object
5.6.9.1 Getting All Two-Loci P-Values in a Dictionary
5.6.9.2 Getting P for Two Markers
5.6.9.3 Getting Adjusted P for Two Markers
5.6.9.4 Getting Bonferonni P for Two Markers
5.6.9.5 Getting Neg Log10 of All Two-Loci P Values in a Dictionary
5.6.9.6 Getting Neg Log10 P for Two Markers
5.6.9.7 Getting Neg Log10 Adjusted P for Two Markers
5.6.9.8 Getting Neg Log10 Bonferonni P for Two Markers
5.6.9.9 Getting Detailed Split Information for Two Markers
5.6.10 Using the P-Value plot
5.6.10.1 Getting P-Values
5.6.10.2 Getting Simes P-Values
5.6.10.3 Setting the Simes Window
5.6.10.4 Getting FDR (aP)
5.6.10.5 Getting all P-Values as a Spreadsheet
5.6.10.6 Getting an Allele Frequency Spreadsheet for a Specific Column
5.6.11 Getting and Setting Tree Options
5.6.11.1 Setting the Minimum Elements for Splitting
5.6.11.2 Setting the Number of Threads
5.6.11.3 Setting the P Value Threshold
5.6.11.4 Setting the Pairwise Threshold
5.6.11.5 Setting the P Threshold Type
5.6.11.6 Setting the Minimum Haplotype Frequency
5.6.11.7 Setting the Haplotype Estimation Method
5.6.11.8 Setting the Segmenting Algorithm
5.6.11.9 Setting the Maximum Segments
5.6.11.10 Setting Resample Iterations
5.6.11.11 Setting Linear Regression
5.6.11.12 Setting Use Missing Values Option
5.6.11.13 Setting Non-Genetic Splits
5.6.11.14 Setting Genotype Splits
5.6.11.15 Setting Haplotype Splits
5.6.12 Creating a Tree Model
5.6.13 Importing a Legacy Tree Model
5.6.14 Tree Model Commands
5.6.14.1 Get Variable Frequencies
5.6.14.2 Get Tree Predictions
5.6.14.3 Get Tree Variables
5.6.14.4 Get Correlation Table
5.6.14.5 Get Correlation Plot
5.6.14.6 Get Observation Distance Matrix Unsorted
5.6.14.7 Get Observation Distance Matrix Sorted by First Principal Component
5.6.14.8 Get Observation Distance Sorted by Similarity to One Observation
5.6.15 Using the Distance Matrix Object
5.6.15.1 Get the Observation Label for a Distance Matrix Plot
5.6.15.2 Get the Observation Number for a Distance Matrix Plot
5.6.15.3 Get the Rank Index for a Distance Matrix Plot
5.6.15.4 Get the Distance Values by Row Number for a Distance Matrix Plot
5.6.15.5 Get the Distance Values by Rank Index for a Distance Matrix Plot
5.6.16 Applying a Tree Model
5.6.17 Copy Number Analysis
5.6.18 Importing Raw Copy Number Values
5.6.19 Performing LogR Association Tests and PCA
5.6.20 Performing Regression
5.6.21 Output a C File
5.6.22 Prompting the User for Input
5.6.23 Text Viewer
5.6.23.1 Getting the text
5.6.23.2 Saving text to a file
5.6.24 Regression Results
5.6.24.1 Getting the text
5.6.24.2 Saving text to a file
5.6.24.3 Getting the covariates
5.6.24.4 Getting the markers
5.6.24.5 Getting the interactions
5.6.25 Navigator Object Selection
5.6.25.1 Selecting a Spreadsheet
5.6.25.2 Selecting a Tree model
5.7 S-PLUS Integration
5.7.1 S-PLUS Desktop Integration
5.7.2 S-PLUS Client/Server 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
6.2.1 Dependent or Independent Variable?
6.2.2 Selecting a Dependent
6.2.3 Deactivating Unwanted Columns
6.2.4 Sorting Records
6.2.5 Plotting Individual Columns
6.2.6 Activating - Deactivating Row Data
6.2.7 Picking Random Record Sets
6.3 The File Menu
6.3.1 Save As - Exporting Data
6.3.2 Save As Comma-Delimited Text File
6.3.3 Save As DSF File
6.3.4 Save As PED/MAP Files
6.3.5 Save Family Data
6.3.6 Apply Gene Marker Map
6.3.7 Join Spreadsheet on Row Labels
6.3.8 Join Spreadsheets With Uneven Row Numbers
6.3.9 Join family-indexed spreadsheets
6.3.10 Join Spreadsheets by Sorting
6.3.11 Import a Legacy Tree Model
6.3.12 Closing the File
6.4 The Edit Menu
6.4.1 Row
6.4.1.1 Activate All
6.4.1.2 Invert Selection
6.4.1.3 Select Subset
6.4.1.4 Subset Spreadsheet
6.4.2 Column
6.4.2.1 Activate All
6.4.2.2 Inactivate All
6.4.2.3 Invert Selection
6.4.2.4 Select Columns by Chromosome/Region Range
6.4.2.5 Find
6.4.2.6 Subset Spreadsheet
6.5 The Analysis Menu
6.5.1 Interactive Tree Analysis
6.5.2 Create a Multiple-Tree Model
6.5.3 Apply a Tree Model
6.5.4 Regression Analysis
6.5.5 Plot Numeric Columns
6.6 The Genetics Menu
6.6.1 Genetic Association Tests
6.6.2 Marker Statistics
6.6.3 Principal Component Analysis
6.6.4 EM Haplotype Frequency Estimation
6.6.5 HWE Plot
6.6.6 LD Plot
6.6.7 PBAT Family-Based Analysis
6.6.8 Runs of Homozygosity
6.6.9 Infer Missing Genotypes
6.7 The Help Menu
II Recursive Partitioning
7 Interactive Tree Analysis
7.1 Tree Analysis Overview
7.2 Setting Options for Tree Analysis
7.2.1 The Tree Tab
7.2.1.1 Minimum Elements per Child:
7.2.1.2 Segmenting Algorithm:
7.2.1.3 Max Segments:
7.2.1.4 Parallel Threads:
7.2.1.5 Resampling Iterations
7.2.1.6 P Value Threshold:
7.2.1.7 Use Missing Values as Predictors (Impute Missing Data for HTR)
7.2.1.8 Linear/Logistic Regression:
7.2.1.9 Non-Genetic Splits
7.2.1.10 Genotype Split
7.2.1.11 Haplotype Trend Regression
7.2.1.12 Fixed Window Size
7.2.1.13 Ignore Marker Mapping
7.2.1.14 Window Size Using Genetic Distance of ____ Units
7.2.1.15 Marker Window Size
7.2.1.16 Minimum Frequency
7.2.1.17 Estimate Frequencies Using CHM or EM
7.2.2 The Node View Tab
7.2.2.1 What the Node Values Mean
7.2.3 The Linkage Disequilibrium Parameters Tab
7.2.3.1 Linkage Disequilibrium CHM vs. EM
7.2.3.2 Hardy Weinberg Correction when Both Markers are Biallelic
7.2.3.3 Use Patient Data Containing Missing Values
7.2.3.4 Maximum EM Iterations
7.2.3.5 EM Convergence Tolerance
7.3 Working with Nodes
7.3.1 Node Pop-up Menu Selections
7.3.1.1 Split Node
7.3.1.2 Manual Split
7.3.1.3 Collapse/Expand
7.3.1.4 Recursive Split
7.3.1.5 Spreadsheet
7.3.1.6 Resample
7.3.1.7 Visualize Genetics
7.3.2 Visualize Split Data
7.3.3 Visualize Split Data->Multiple Tree Clustering
7.3.4 Visualize Split Data->Histogram
7.3.5 Showing Split Data
7.3.5.1 Linear Regression Splits
7.3.5.2 Logistic Regression Splits
7.3.5.3 Splits on Continuous Predictors
7.3.5.4 Splits on Categorical Predictors
7.4 Manually Splitting Nodes
7.4.1 P Value Plots
7.4.2 Define Split
7.4.3 Don’t Split
7.4.4 Manual Split with Regression
7.4.5 Using the Tree and Manual Split Window Together
7.5 Defining Splits
7.5.1 The Split Point
7.5.2 The Split Point Controls the Node Information
7.5.3 Smoothing the Data Points
7.5.4 Refined or Course Data Points
7.5.5 Zooming into a Specific Region
7.5.6 Adding Linear Regression
7.5.7 Categorical Predictors
7.6 The File Menu
7.6.1 File->Print tree
7.6.2 File->Save Tree Image
7.6.3 File->View Predictions (In-Sample)
7.6.4 File->Output C Code
7.6.5 File->Close
7.7 The Tree Menu
7.7.1 Tree->Options
7.7.2 Tree->Subset Spreadsheet
7.7.3 Tree->Subset Tree
7.7.4 Tree->Extend Current Tree Randomly
7.7.5 Tree->Search Tree
7.7.5.1 Tree->SearchTree->Find Observation
7.7.5.2 Tree->SearchTree->Find Node
7.7.5.3 Tree->SearchTree->Select Node by Threshold
7.7.5.4 Tree->SearchTree->Highlight All Nodes
7.7.5.5 Tree->SearchTree->UnHighlight All Nodes
7.8 The Font Menu - Resizing and Formatting Tree View
7.8.1 Font->Size
7.8.2 Font->Family
8 Prediction Recipes
8.1 Training and Validation Recipe
8.2 Predicting An Unknown Response
8.2.1 Modifying a Copy of Data
8.2.2 Converting to a GHD File
8.2.3 Create a Subset With BP Readings
8.2.4 Create Random Trees From Initial Dataset
8.2.5 Invert Data to Create Dataset With Missing BP
8.2.6 Applying A Multitree Model To Make Predictions
9 Random Tree Generation
9.1 Random Tree Overview
9.2 Creating a Random Tree Model
9.3 Multitree Model Browsing - Tree View
9.3.1 Multitree Model – Tree List
9.3.2 Multitree Model – Variable List
9.3.2.1 Sorting
9.3.2.2 Subset
9.3.2.3 Variables->View Variable Usage
9.3.2.4 Variables->View Variable Frequency
9.3.2.5 Viewing Variable Correlations
9.3.3 File->Analyze Current Tree Tools
9.3.4 Predictions (InSample)->View Average Tree In-Sample Predictions
9.3.5 Predictions (InSample)->Save All Tree In-Sample Predictions to CSV File
9.3.6 Save “C” Prediction Program
9.3.7 Close
9.3.8 Help
10 Multivariate Tree Analysis
10.1 Multivariate Analysis Overview
10.2 Using More Than One Dependent Variable
10.2.1 Continuous Multivariate Response
10.2.2 Binary and/or Categorical Multivariate Response
10.2.3 Multivariate Multiple Tree Clustering
10.2.4 File->Output C Code
11 Histogram Node Analysis
11.1 Histogram Overview
11.2 Viewing Split Data Histograms
11.2.1 Creating Histograms
11.2.2 Visualizing Node Relationships
11.2.3 Changing Bins
11.2.4 Zooming or Rubber Banding Data
11.2.5 Menus
11.2.6 File->Print
12 The Observation Distance Matrix
12.1 Observation Distance Matrix Overview
12.1.1 Creating an Observation Distance Matrix
12.1.2 The Observation Distance Matrix
12.1.3 Set Axes
12.1.4 Stop Calculation/Stop Refresh and Restore Calculation/Restore Refresh
12.1.5 Copy to Clipboard
12.1.6 Creating a Spreadsheet or Tree view from the Matrix Plot
12.1.7 Zoom Mode
12.1.8 Modify Color Scaling
12.1.9 Effect of Clicking on the Plot
12.1.10 Color Drop Down Menu
12.2 Viewing Observation Distance Matrix
12.2.1 Viewing Spreadsheets or Trees of Subsets
12.2.2 Zooming-In on a Subset of the Distance Matrix Plot
12.2.3 Narrowing the Distance Range
12.2.4 Menus
12.3 Printing and Saving the Observation Distance Matrix
12.3.1 Save Image or Print
12.3.2 The Menus
12.3.3 File->Save Obs. Distance Matrix (Sorted)
13 The Correlation Interaction View
13.1 Correlation Interaction Overview
13.1.1 Pick Wanted Variables
13.2 Viewing Correlation Interactions
13.2.1 The Correlation Interaction View
13.2.2 The Upper Triangle
13.2.3 The Lower Triangle
14 Linkage Disequilibrium View
14.1 Linkage Disequilibrium Overview
14.2 Plotting Linkage Disequilibrium
14.2.1 Stop Calculation/Stop Refresh and Resume Calculation/Resume Refresh
14.2.2 Copy to Clipboard
14.2.3 Plot Visual: Color or Black and White
14.2.4 Fill Mode
14.2.5 Zoom Mode
14.2.6 Click on Graph
14.2.7 Modify Color Scaling
14.3 The File Menu
14.3.1 Create Bitmap
14.3.2 Print Image
14.3.3 Summarize Data for All Points to CSV File
14.3.4 Output Genotypes for Current Point to CSV File
14.3.5 Output Genotype Combinations for Current Point
14.3.6 Output Allele Counts for Current Point
14.3.7 Output Allele Combinations for Current Point
14.3.8 View Carlson-Method SNP Tags
14.4 LD Computation
14.4.1 LD Computation for D prime
14.4.2 LD Computation for Quick Mode
15 Hardy Weinberg Equilibrium View
15.1 Plotting Hardy Weinberg
15.1.1 Hardy Weinberg Equilibrium Plot
15.1.2 Reset View
15.1.3 Copy to Clipboard
15.1.4 Axis Selector
15.1.5 Zooming into the Graph
15.1.6 File Menu
15.1.7 Create Bitmap
15.1.8 Print Image
15.1.9 Summarize All Data to CSV File
15.1.10 Output All Allele Tables to CSV File
15.1.11 Output All Genotype Tables to CSV File
15.1.12 Hardy-Weinberg Equilibrium computation
16 P-Value and Spreadsheet Plots
16.1 Plotting P-Values and Spreadsheet Columns
16.2 P-Value Plot Types
16.2.1 P-Values Sorted by Var # from the Manual Split Window
16.2.2 FDR and P-Values from the Manual Split Window
16.2.3 P-Values Resulting from Regression Analysis Using a Moving Window
16.2.4 Spreadsheet Column Plots
16.3 Plot Functions
16.3.1 Clicking at a Point to Show Values
16.3.2 Reset View
16.3.3 Copy to Clipboard
16.3.4 View Regression Results (Regression Plots Only)
16.3.5 Axis Selector
16.3.6 Logarithm Mode Selector (Spreadsheet Plots Only)
16.3.7 Zooming into the Graph
16.4 The File Menu
16.4.1 Create Bitmap
16.4.2 Print Image
16.4.3 P-Value Spreadsheet
17 Haplotype Regression and the Allele Table
17.1 Plotting Haplotype Regression
17.1.1 Haplotype Regression
17.1.2 Obtaining a Haplotype Regression
17.1.3 Viewing the Details of the Regression
17.1.4 Residual Spreadsheet
17.1.5 Regression Statistics
17.1.5.1 Overall Statistics
17.1.5.2 Regressor Statistics
17.1.5.3 Left-Out Regressors
17.1.5.4 Table of Haplotypes
17.1.5.5 Parameters
17.2 Displaying the Allele Table
17.2.0.6 Display Allele Table
18 Genetic Association Tests
18.1 Genetic Association Tests Overview
18.2 Genetic Models and Other Genetic Tests
18.2.1 Basic Allelic Tests
18.2.2 Genotypic Tests
18.2.3 Additive Model
18.2.4 Dominant Model
18.2.5 Recessive Model
18.3 Test Statistics
18.3.1 Correlation/Trend Test
18.3.2 Armitage Trend Test
18.3.3 Exact Form of Armitage Test
18.3.4 (Pearson) Chi-Squared Test
18.3.5 Fisher’s Exact Test
18.3.6 Odds Ratio with Confidence Limits
18.3.7 Analysis of Deviance
18.3.8 F-Test
18.4 Missing Values
18.4.1 Using Missing Values for Genotypes
18.4.2 Missing Values in a Case/Control Variable
18.5 Multiple Testing Corrections
18.5.1 Bonferonni Adjustment
18.5.2 False Discovery Rate
18.5.3 Permutation Testing
18.5.3.1 Single Value Permutation Testing
18.5.3.2 Full Scan Permutation Testing
18.6 Correction for Stratification
18.6.1 Correction of Input Data by Principal Components Analysis
18.6.2 Working Premise
18.6.3 The PCA Technique
18.6.4 How Many Components to Use?
18.6.5 A Second Answer
18.6.6 Removing Outlier Subjects
18.6.7 PCA-Corrected Association Testing
18.6.8 Correction of Output Chi-Square Values and P-Values by Genomic Control
18.7 Overall Marker Statistics
18.7.1 Minor Allele Frequency
18.7.2 Output Spreadsheet of DD/Dd/dd genotypes
18.7.3 Call Rate
18.7.4 Hardy-Weinberg Equilibrium P-Value
18.7.5 Fisher’s Exact Test for HWE P-Value
18.7.6 Signed HWE R
18.7.7 Genotype Count Table(s)
18.7.8 Allele Count Table(s)
18.8 Using the Association Test Window
18.8.1 Data Requirements
18.8.2 Available Tabs
18.8.3 The Association Test Parameters Tab
18.8.4 Principal Component Analysis Parameters Tab