Package index • HaploBreedR

Pipeline: Superior Haplotype Discovery

End-to-end and modular tools for functional variant identification, intragenic haplotype assembly, association testing, gate re-application, and run loading. See haplobreed_analysis() for the single-trait pipeline; the remaining functions are the per-step entry points.

haplobreed_analysis(): Single-trait identification of genes carrying superior haplotypes
hbr_check_inputs(): Pre-flight Validation of Inputs
hbr_generate_input_qc_report(): Generate a unified input-QC report
hbr_read_results(): Read finished HaploBreedR results from disk or memory
hbr_gene_carriers(): Carrier status of the superior haplotype at a gene
hbr_regate(): Re-apply the superior-haplotype rule with different settings

Genomic Selection & Breeding Decisions (HGSI)

Two-kernel spectral REML prediction, cross usefulness, multi-locus pyramiding, haplotype-block calling, and parent-set optimization. hbr_fit_models() and hbr_cross_design() are the two halves of the pipeline; hbr_advanced_decision() runs them end to end.

hbr_advanced_decision(): Breeding decisions from HaploBreedR output
hbr_fit_models(): Fit genomic prediction models and rank parents
hbr_cross_design(): Design crosses from a fitted model
hbr_cross_plan(): Plan a cross between named parents
hbr_cross_usefulness(): Analytical Cross Usefulness
hbr_haplotype_blocks(): Haplotype blocks of target loci
hbr_haplotype_block_table(): Haplotype block table from a set of target loci
hbr_pyramid_probability(): Haplotype Pyramiding Probability
hbr_population_size(): Population Size for Recombinant Recovery
hbr_build_grm(): Streamed Genomic Relationship Matrix
hbr_reml_two_kernel(): Spectral Two-Kernel REML
hbr_trait_conflicts(): Multi-Trait Haplotype Breeding Conflicts

Publication Figures & Visualisation

High-level ggplot2 publication graphics for candidate genes, haplotype networks, gene models, LD structure, cross rankings, and model validation.

hbr_plot_haplotype(): Plot haplotype boxplot with summary table
hbr_plot_gene_structure(): Plot gene structure for one or more genes
hbr_plot_haplotype_network(): Plot a haplotype network for one or more genes
hbr_plot_cross_ranking(): Plot cross ranking by usefulness vs mid-parent index
hbr_plot_cv_forest(): Forest plot of cross-validation comparisons

Variant Annotation & Population Genetics

LD decay estimation, GFF3 gene parsing, genomic-region interval intersection, and GO term over-representation.

hbr_annotate_regions_with_genes(): Annotate LD regions with genes
hbr_read_gff3_genes(): Parse gene features from a GFF3 into a data.table
hbr_go_enrichment(): GO term enrichment across a set of genes

Manuscript Tables & Reporting

Formatted multi-sheet Excel manuscript tables built from a single pipeline run.

hbr_build_manuscript_tables(): Build a manuscript-ready multi-sheet Excel workbook from a pipeline run

Reference Data, Themes & Lookups

Genetic linkage maps, crop genome metadata, colour palettes, and ggplot2 themes shipped with the package.

hbr_rice_genetic_map(): Bundled rice genetic map anchors
hbr_crop_lookup(): Common crops mapped to their Ensembl Plants species and assembly
hbr_palette(): Return `n` colours from a named palette
hbr_palette_names(): Names of the built-in colour palettes
hbr_theme(): Return a named HaploBreedR ggplot2 theme
hbr_theme_names(): Names of the built-in ggplot2 themes

S3 methods for pipeline and fit objects

Print, summary, and plot methods for the classed objects the pipeline and the fit/design step return.

print(<hbr_run>): Print an hbr_run object
summary(<hbr_run>): Summary of an hbr_run object
plot(<hbr_run>): Plot an hbr_run object
print(<hgsi_fit>): Print an hgsi_fit object
summary(<hgsi_fit>): Summarise an hgsi_fit object
print(<hgsi_advanced>): Print an hgsi_advanced object
summary(<hgsi_advanced>): Summarise an hgsi_advanced object
plot(<hgsi_advanced>): Plot an hgsi_advanced object
print(<hbr_regate>): Print an `hbr_regate` result
print(<hbr_blocks>): Print an `hbr_blocks` result

S3 methods for reference and QC objects

Print methods for the small classed objects returned by the input validation and reference-loading layers.

print(<hbr_reference>): Print an hbr_reference object
print(<hbr_sequence_qc>): Print a sequence-resource QC report
print(<hbr_compat_report>): Print a genotype-reference compatibility report
print(<hbr_id_report>): Print an individual-ID match report
print(<hbr_genotype>): Print an hbr_genotype object