1. Genotype input | Converting from other formats | Filtering markers with filter_geno() | 2. The genetic map | 3. The simulation grammar | Every layer | Layer options | Replications and per-trait proportions | One call instead of a pipe | Fine control: fixed loci, phase, means, subsets | 4. Genetic architectures | Independent | Pleiotropy with a target genetic correlation | Linkage disequilibrium | Combining architectures | 5. Breeding populations | Crossing, selfing, doubled haploids | Recurrent selfing | Reproducibility | Phenotyping a pedigree | 6. Inspecting a simulation | 7. Output | In memory | Written to disk | 8. Transcriptome and expression-mediated phenotypes | Simulating expression | A phenotype from expression | Genetic and environmental mediation | Without genotypes | Reusing an architecture in a new population | Calibrating to observed expression | RNA-seq counts | 9. Original implementation of create_phenotypes | Session information

Why base pairs are not enough | synthetic_map() | What the model does | Tuning it | Using a real map | How the map changes results | Session information

Before you start: you need a genetic map | Founders | Working with a Population | Your first cross | Selfing | Doubled haploids | Backcrossing | Recurrent selfing: from an F1 to inbred lines | Checking the simulation is doing what you think | Reproducibility | Phenotyping a pedigree | A complete example | Common problems | Session information

Single trait | Pleiotropy | Partial pleiotropy | Spurious pleiotropy (LD) | Choosing the QTNs yourself | Variance explained by each QTN | Output formats | Reading genotypes from files | Residual correlation | Not yet in the grammar

The example data | The genetic map | Reading genotype data | Simulating phenotypes: the grammar | Dominance, epistasis and variance QTL | Multiple traits and genetic correlation | Linked, not pleiotropic: the "ld" architecture | Combining architectures | One call instead of a pipe | Writing results | Multi-generation crosses | Original implementation of create_phenotypes | Session information

Load Sample Data set | Single Trait | Multiple Traits: Pleiotropy Architecture | Multiple Traits: Partial Pleiotropy Architecture | Multiple Traits: Spurious Pleiotropy Architecture | Multiple Traits: Partial Pleiotropy Architecture with other useful parameters | Using Selected Markers to be QTN | Using Multiple Marker Data Files