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
 18.6 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
  18.8.5 Overall Marker Statistics Tab
  18.8.6 Processing
  18.8.7 Spreadsheet Outputs
 18.9 Using the Separate Principal Components Analysis Window
  18.9.1 Data Requirements
  18.9.2 Processing
  18.9.3 Spreadsheet Outputs
 18.10 Using the Separate General Marker Statistics Window
  18.10.1 Data Requirements
  18.10.2 Processing