26.1 Split-Prediction Methodology
 26.2 Normally Distributed Response Binomial Predictor
  26.2.1 Univariate Case
  26.2.2 Multivariate Case
 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)
  26.7.1 Technical details
  26.7.2 Haplotype Trend Regression (HTR)
 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)
  26.11.1 P-value Plot
  26.11.2 Residual Spreadsheet
  26.11.3 Linear Regression Statistical Output Viewer
  26.11.4 Overall Statistics
  26.11.5 Regressor Statistics
  26.11.6 Left-Out Regressors
  26.11.7 Table of Haplotypes
  26.11.8 Parameters
 26.12 Binomially Distributed Response Binary Predictor
  26.12.1 Univariate Case
  26.12.2 Multivariate Case
 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)
  26.18.1 P-value Plot
  26.18.2 Residual Spreadsheet
  26.18.3 Logistic Regression Statistical Output Viewer
  26.18.4 Overall Statistics
  26.18.5 Regressor Statistics
  26.18.6 Left-Out Regressors
  26.18.7 Table of Haplotypes
  26.18.8 Parameters
  26.18.9 Caveats
 26.19 Categorical Response
 26.20 The False Discovery Rate and the Simes Method
  26.20.1 The False Discovery Rate
  26.20.2 Simes’ Method
 26.21 Permutation Test Methodology
  26.21.1 Single Value Permutations
  26.21.2 Full Scan Permutations
 26.22 Methods for the Genetic Association Tests
  26.22.1 Correlation/Trend Test
  26.22.2 Armitage Trend Test
  26.22.3 Exact Form of Armitage Test
  26.22.4 (Pearson) Chi-Squared Test
  26.22.5 Fisher’s Exact Test
  26.22.6 Odds Ratio with Confidence Limits
  26.22.7 Analysis of Deviance
  26.22.8 The F-Test
  26.22.9 The T-Test
 26.23 Formulas for Principal Components Analysis
  26.23.1 Motivation
  26.23.2 Technique
  26.23.3 Applying the PCA Corrections
  26.23.4 Formulas for PCA Normalization
 26.24 Methods for Obtaining General Marker Statistics
  26.24.1 Fisher’s Exact Test for HWE P-Value
  26.24.2 Signed HWE R