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{ "page": "plot_feature_track", "title": "Plot a FeatureTrack object", "topics": [ "plot_feature_track" ] }, { "page": "plot_gene", "title": "Plot a gene structure", "topics": [ "plot_gene" ] }, { "page": "plot_gene_length_distribution", "title": "Plot gene annotation feature length distributions", "topics": [ "plot_genepred_length_distribution", "plot_gene_length_distribution" ] }, { "page": "plot_hap_pheno", "title": "Plot phenotype values grouped by haplotype", "topics": [ "plot_hap_pheno" ] }, { "page": "plot_hap_refined", "title": "Plot phenotype distributions for refined haplotypes", "topics": [ "plot_hap_refined" ] }, { "page": "plot_hap_variant", "title": "Plot gene variants and haplotype table", "topics": [ "plot_hap_variant" ] }, { "page": "plot_ld_block", "title": "Plot a triangular LD heatmap", "topics": [ "plot_ld_block" ] }, { "page": "plot_pheno", "title": "Plot phenotype distributions", "topics": [ "plot_pheno" ] }, { "page": "plot_refined_hap_pheno", "title": "Plot 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{ "page": "plot_variant_effect", "title": "Plot phenotype effect size of each natural variant", "topics": [ "plot_variant_effect" ] }, { "page": "plot_variant_pheno", "title": "Plot phenotype values grouped by a single variant genotype", "topics": [ "plot_variant_pheno" ] }, { "page": "plot_variant_track", "title": "Plot a VariantTrack object", "topics": [ "plot_variant_track" ] }, { "page": "print.GeneTrackRPhenoPlot", "title": "Print GeneTrackR phenotype plot result", "topics": [ "print.GeneTrackRPhenoPlot" ] }, { "page": "read_bed", "title": "Read a BED file as a FeatureTrack", "topics": [ "read_bed" ] }, { "page": "read_bwg", "title": "Read bedGraph, wig, or bigWig signal tracks", "topics": [ "read_bwg" ] }, { "page": "read_genepred", "title": "Read a GenePred annotation file", "topics": [ "read_genepred" ] }, { "page": "read_gff", "title": "Read a GFF3 file as a FeatureTrack", "topics": [ "read_gff" ] }, { "page": "read_gtf", "title": "Read a GTF file as a FeatureTrack", "topics": 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Verify sample matching explicitly", "Step 4. Test the primary haplotype-phenotype association", "Step 5. Compare traits and choose the statistical settings", "Step 6. Control phenotype-association plot appearance", "Step 7. Test a single variant against phenotype", "Step 8. Pass the same objects downstream", "Session information" ], "created": "2026-08-29 08:25:17", "modified": "2026-09-01 07:51:36", "commits": 7 }, { "source": "linkage-disequilibrium.Rmd", "filename": "linkage-disequilibrium.html", "title": "Linkage disequilibrium analysis", "author": "Shuchao Ren", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Step 1. Prepare VCF genotypes and annotation", "Step 2. Compute the primary twelve-variant LD-gradient example", "Step 3. Inspect the LDTrack object and pairwise statistics", "Step 4. Inspect the LD matrix and quantify the LD gradient", "Step 5. Draw the triangular LD heatmap", "Step 6. Add gene structure and natural-variant markers", "Step 7. Compare the LD-gradient, low-LD, and two-variant regions", "Step 8. Control samples, variant types, LD methods, and genotype retention", "Select samples", "Select variant types", "Retain the dosage matrix when needed", "Use D-prime cautiously", "Step 9. Interpret LD and pass the selected region downstream", "Session information" ], "created": "2026-08-29 08:55:21", "modified": "2026-09-01 07:51:36", "commits": 7 }, { "source": "haplotype-refinement.Rmd", "filename": "haplotype-refinement.html", "title": "Phenotype-guided haplotype refinement", "author": "Shuchao Ren", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Step 1. Prepare the original haplotypes and phenotype data", "Step 2. Inspect genotype similarity and phenotype correspondence before refinement", "Step 3. Refine haplotypes using protein_content", "Step 4. Inspect the HapRefined object", "Step 5. Inspect pairwise tests and merge decisions", "Step 6. Plot the refined haplotype structure", "Keep the original haplotypes inside refined blocks", "Collapse each refined group to one row", "Step 7. Plot phenotype distributions after refinement", "Step 8. Evaluate trait choice and refinement thresholds", "A strongly haplotype-associated trait may preserve all groups", "A negative-control trait can collapse all groups", "Multiple traits make the refinement criterion stricter", "Step 9. Interpret and reuse refined haplotypes", "Session information" ], "created": "2026-08-29 08:55:21", "modified": "2026-09-01 07:51:36", "commits": 7 }, { "source": "variant-effect.Rmd", "filename": "variant-effect.html", "title": "Variant effect analysis", "author": "Shuchao Ren", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Step 1. Prepare GeneA variants and phenotype data", "Step 2. Understand genotype coding before interpreting effect direction", "Step 3. Calculate the primary protein-content effect scan", "Step 4. Inspect the result object", "Step 5. Rank candidate variants", "Step 6. Interpret tied effects together with genotype structure and LD", "Step 7. Inspect signed effects carefully", "Step 8. Validate varA03 with a direct single-variant phenotype plot", "Step 9. Compare multiple traits and connect downstream evidence", "Session information" ], "created": "2026-08-29 08:55:21", "modified": "2026-09-01 07:51:36", "commits": 7 }, { "source": "complete-workflow.Rmd", "filename": "complete-workflow.html", "title": "Complete candidate-locus workflow", "author": "Shuchao Ren", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Step 1. Define and read the inputs", "Step 2. Validate and summarize the core objects", "Step 3. Inspect the locus in a browser-like view", "Step 4. Retrieve the gene-body variants", "Step 5. Construct and visualize the GeneA haplotypes", "Step 6. Test phenotype associations", "Step 7. Inspect the regional LD gradient", "Step 8. Refine haplotypes with phenotype evidence", "Step 9. Rank variant effects and integrate the evidence", "Step 10. Export results and scale the workflow to real datasets", "Installation", "Session information" ], "created": "2026-08-29 08:56:53", "modified": "2026-09-01 07:51:36", "commits": 7 }, { "source": "export-results.Rmd", "filename": "export-results.html", "title": "Export and reproducibility", "author": "Shuchao Ren", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Step 1. Prepare output directories and representative objects", "Step 2. Export genomic track files", "Annotation tracks", "Signal tracks", "Variant tracks", "Step 3. Save figures as PDF and PNG", "Step 4. Export analysis tables", "Step 5. Export the LD matrix cleanly", "Step 6. Optionally collect tables in an Excel workbook", "Step 7. Save complete GeneTrackR objects with RDS", "Step 8. 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