II Recursive Partitioning
Part 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
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
