Introduction | Notation and Models | Model 0 - Environment-only Model | Model 1 - Gene-only Model | Model 2 - GxE Interaction Model | Model 3 - EG Model | Model 4 - Case-only Model | Model 5 - Control-only Model | Steps to Run a GWEIS | Step 1: Preparing the Data | Genetic Data | Subject Data | Step 2: Fitting the Base Model | Continuous Phenotype | Dichotomous Phenotype | Step 3: Allocating Memory for the GWEIS | Step 4: Running the GWEIS | Step 5: Processing the Results | SNP Information and Allele Frequency | Model 1 Output: bg_ge | Model 2 Output: bg_gxe, bgxe, joint | Models 3–5 Output: bg_eg, bg_case, bg_ctrl

Format 1 | Format 1.1 | Format 1.2 | Format 2 | Format 2.1 | Format 2.2 | Format 3 | Format 3.1 and 3.3 | Format 3.2 | Format 3.4 | Format 4 | Format 4.1 and 4.3 | Format 4.2 and 4.4 | Minimizing the data stored

Common section | Binary Dosage Additional Information | VCF File Additional Information | GEN File Additional Information

Introduction | Legacy File Formats | Formats 1, 2, and 3 (three-file layout) | Format 1 | Format 2 | Format 3 | Format 4 (single-file layout) | Compressed storage (subformats x.2 and x.4) | Functions Overview | Converting VCF Files | Example files | Basic conversion | Compressed VCF files | Other VCF formats | snpidformat option | bdoptions — calculating per-SNP statistics | Converting GEN Files | Parameters | snpcolumns | impformat | gz | Merging Legacy Binary Dosage Files | Example | Reading Legacy Binary Dosage Files | getbdinfo | bdapply | getsnp | Working Directly with VCF and GEN Files | VCF files | GEN files | Full Workflow Example

bdmerge

Introduction | Setup | Subject merge | Verifying subject order | SNP merge | Verifying SNP order

Introduction | Setup | getbd5snp | Parameters | Return value | Reading a SNP by index | Reading a SNP by ID | Using getbd5snp in a loop | getbd5snp_buf | Important: R copy-on-modify semantics | Example | getbd5snp_con | Workflow | openbd5con | closebd5con | Choosing a reader

getbdinfo | bdapply | getsnp

Introduction | Example files | Converting a VCF file to Format 5 | Loading Format 5 file information | File and format metadata | Sample information | SNP information | Byte offsets | Reading SNP data | Reading a SNP by index | Reading a SNP by ID | Applying a function to all SNPs

Introduction | GEN file formats | Example files | Converting a GEN file to the Binary Dosage format | Default options | snpcolumns | startcolumn | impformat | chromosome | header parameter | gz | separator | bdfiles | format | subformat | snpidformat | bdoptions | Additional routines | getgeninfo | genapply

Introduction | Example files | Converting a VCF file to the Binary Dosage format | Minimac files | Uncompressed VCF files | No imputation information file | Using the imputation information file | Compressed VCF files | Checking the files | Other VCF file formats | Other vcftobdlegacy options | format and subformat options | snpidformat | bdoptions | Additional routines | getvcfinfo | vcfapply

Available test statistics | Return values | Example | Results

Overview | Example data | Step 1: Fit the base model | Step 2: Allocate memory | Step 3: Test each candidate covariate | Results | Verification against standard GLM

Overview | Example data | Step 1: Fit the base model | Step 2: Allocate memory | Step 3: Test each candidate covariate | Results | Verification against standard GLM

Overview | Example data | Step 1: Fit the base model | Step 2: Allocate memory | Step 3: Test each candidate covariate | Results | Verification against statmod