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Manual

TODO

  • links
  • add explanations
  • add examples

Main

  • GBInput: Struct for input data.
  • checkinputs: Check input data.
  • loadgenomesphenomes: Load genomic and phenomic data.
  • loadcvs: Load cross-validation data.
  • loadfits: Load model fits.
  • prepareinputs: Prepare input data.
  • prepareoutprefixandoutdir: Prepare output prefix and directory.
  • cv: Perform cross-validation.
  • fit: Fit models.
  • predict: Make predictions.
  • gwas: Perform genome-wide association studies.
  • submitslurmarrayjobs: Submit SLURM array jobs.
  • plot: General plotting function.

Core Data Structures

  • AbstractGB: Abstract type for genomic breeding data.
  • Genomes: Struct for genomic data.
  • Phenomes: Struct for phenomic data.
  • Trials: Struct for trials data.
  • SimulatedEffects: Struct for simulated genetic effects.
  • TEBV: Struct for trial-estimated breeding values.
  • Fit: Struct for genotype-to-phenotype models.
  • CV: Struct for cross-validation of genotype-to-phenotype models.

General Functions

  • clone: Clone a struct.
  • hash: Compute the hash of a struct.
  • ==: Check equality of structs.
  • checkdims: Check dimensions of genomic data.
  • dimensions: Get dimensions of genomic data.
  • loci_alleles: Get loci alleles.
  • loci: Get loci.
  • plot: Plot genomic data.
  • slice: Slice genomic data.
  • filter: Filter genomic data.
  • tabularise: Convert genomic data to a tabular format.
  • summarise: Summarise genomic data.

Simulation Functions

  • simulategenomes: Simulate genomic data.
  • simulateeffects: Simulate genetic effects.
  • simulategenomiceffects: Simulate genomic effects.
  • simulatetrials: Simulate trials data.

Phenotype Analysis Functions

  • countlevels: Count levels in phenomic data.
  • @string2formula: Convert string to formula.
  • trialsmodelsfomulae!: Generate trial models formulae.
  • analyse: Analyse phenomic data.
  • extractphenomes: Extract phenomic data.
  • @stringevaluation: Evaluate string expressions.
  • addcompositetrait: Add composite trait to phenomic data.

Phenotype Analysis Functions

  • impute: Impute missing genotype data-points

Input/Output Functions (GenomicBreedingIO)

  • levenshteindistance: Compute Levenshtein distance for fuzzy matching.
  • isfuzzymatch: Check for fuzzy matches.
  • readjld2: Read JLD2 files.
  • readdelimited: Read delimited text files.
  • readvcf: Read VCF files.
  • writejld2: Write JLD2 files.
  • writedelimited: Write delimited text files.
  • writevcf: Write VCF files.

Genomic Prediction Functions (GenomicBreedingModels)

  • metrics: Compute metrics for model evaluation.
  • extractxyetc: Extract features and targets for modelling.
  • predict: Make predictions using trained models.
  • grmsimple: Compute genomic relationship matrix (simple).
  • grmploidyaware: Compute genomic relationship matrix (ploidy-aware).
  • gwasprep: Prepare data for GWAS.
  • gwasols: Perform GWAS using ordinary least squares.
  • gwaslmm: Perform GWAS using linear mixed models.
  • loglikreml: Compute log-likelihood for REML.
  • gwasreml: Perform GWAS using REML.
  • square, invoneplus, log10epsdivlog10eps, mult, addnorm, raise: Utility functions for transformations.
  • transform1, transform2, epistasisfeatures, @string2operations, reconstitutefeatures: Functions for feature engineering.
  • bglr, bayesian: Bayesian genomic prediction models.
  • turing_bayesG, turing_bayesGs, turing_bayesGπ, turing_bayesGπs, turing_bayesL, turing_bayesLs, turing_bayesLπ, turing_bayesLπs, turing_bayesT, turing_bayesTπ, turing_bayesG_logit: Turing Bayesian models.
  • ols, ridge, lasso, bayesa, bayesb, bayesc: Linear and Bayesian regression models.
  • validate: Validate models.
  • cvmultithread!, cvbulk: Cross-validation functions.
  • cvperpopulation, cvpairwisepopulation, cvleaveonepopulationout: Cross-validation strategies.

Plotting Functions (GenomicBreedingPlots)

  • PlotsGB: General plotting functions.
  • DistributionPlots: Distribution plots.
  • ViolinPlots: Violin plots.
  • CorHeatPlots: Correlation heatmaps.
  • TreePlots: Tree plots.
  • BarPlots: Bar plots.
  • BoxPlots: Box plots.
  • PCBiPlots: Principal component biplots.
  • checkdims: Check dimensions for plotting.
  • labeltofname: Convert labels to filenames.
  • saveplots: Save plots to files.