Package index

Import and the AlphaVarSet object

An AlphaGenome CSV becomes a typed object; every other function takes that object and returns an updated one.

av_import_csv()

Import AlphaGenome Results

av_set_active_score()

Set Active Score Type

av_get_scores()

Extract Active Score Vector

av_overview_summary()

Generate Data-Overview Summary

av_overview_breakdown()

Per-Element Breakdown for a Column

print(<AlphaVarSet>)

Print method for AlphaVarSet

print(<AlphaVarOverview>)

Print method for AlphaVarOverview

print(<AlphaVarReportSpec>)

Print an AlphaVarReportSpec

Annotation

Attach gene and region context to the scored tracks.

av_annotate_genes()

Annotate Variants with Nearest Gene and High-Resolution Genomic Context

av_annotate_regions()

Annotate Variants with Custom Regions (e.g., HARs)

Localization tests

Where does the effect stand out? Each returns a p-value with an effect size, Benjamini-Hochberg corrected, written to $stats$comparisons.

av_calc_enrichment()

Calculate Fisher Enrichment Statistics

av_compare_groups()

Compare Groups: Multi-Group Differential Analysis Engine

av_compare_against_reference()

Compare Against Reference: Many-to-One Differential Analysis

av_compare_target()

Compare One Element vs Rest (Distributional One-vs-Rest Wilcoxon)

av_calc_shift()

Score Shift Sweep: Every Element vs Rest (One-vs-Rest Wilcoxon)

Descriptive metrics

How large, how typical, how concentrated is the effect? Summaries and the specificity index, without a test.

av_summarize()

Summarize an AlphaVarSet by Arbitrary Grouping

av_calc_specificity()

Calculate Effect Specificity Across a Variable

av_element_summary()

Per-Element Statistical Summary Across One Variable

Prioritization and target genes

Which variant should be followed up, and which gene does it act on?

av_prioritize()

Prioritize Variants by Transparent Multi-Criteria Ranking

av_map_targets()

Map Each Variant to a Target Gene (Two-Tier V2G Annotation)

Data operations

Choose the slice to ask about. These change the data basis and therefore reset cached statistics.

av_subset()

Subset an AlphaVarSet Object

av_get_top()

Get Top Entries or Genes

av_as_subsets()

Split AlphaVarSet into Subsets by Group

av_tag_cohort()

Tag filtered variants as a named cohort

av_recode_groups()

Recode Groups for Comparison Analysis

av_get_intersection()

Get Intersection of Top Elements Across N Groups

av_get_filter_history()

Get Filter History as a Data Frame

av_print_breadcrumbs()

Print Filter History as Breadcrumbs

av_export_input_ids()

Widget IDs for the Figure Export Controls of a Plot Card

Visualization

Plots render from the object’s current state.

av_plot_distribution()

Plot Score Distributions

av_plot_comparison()

Plot Group Comparison (Differential Analysis)

av_plot_target()

Plot Target vs Background Score Distribution

av_plot_enrichment()

Plot Enrichment Results

av_plot_specificity()

Plot Variant Specificity

av_plot_priority()

Plot Top Variants by Priority Rank

av_plot_locus()

Plot Genomic Locus (Manhattan-style)

av_plot_interval()

Plot Scored Interval (UCSC Genome Browser Style)

av_plot_annotation()

Visualize Genomic Annotation Landscape

Reporting

Reproducible HTML/PDF reports, from the default template or a custom spec.

av_create_report()

Create Analysis Report

av_export_pdf()

Export HTML Report as PDF

av_report_template_default()

Default Report Template

av_report_add_block()

Add a Block to a Report Spec

av_report_remove_block()

Remove a Block from a Report Spec

av_report_registry()

Report Block Registry

av_report_save_template()

Save a Report Template to YAML

av_report_load_template()

Load a Report Template from YAML

validate_report_spec()

Validate an AlphaVarReportSpec

Interactive app

The code-free route through the same functions.

av_run_shiny()

Launch AlphaVaR Interactive Explorer

av_explore()

Explore AlphaGenome Variant Scores

Theming and plot helpers

Used by the app and the plot functions; rarely called directly.

av_theme_alpha()

AlphaVaR Publication Theme

render_av_plot()

Render a ggplot with Context-Aware Scaling (Shiny only)

render_av_plotly()

Render a plotly with Context-Aware Scaling (Shiny only)

av_finalize_plotly()

Finalize a ggplot for plotly rendering with mathematical axis labels

Shiny building blocks

UI and server components of the app.

av_ui_tab_intro()

Create a Tab Introduction Text Block

av_ui_plot_card()

Create a Plot Card with Help Popover for Shiny

av_ui_plot_header()

Create a Card Header with Help Popover

av_ui_help_popover()

Create a Standalone Help Popover Icon

av_ui_export_panel()

Create the Collapsed Figure-Export Block of a Plot Card

av_ui_report_builder()

Report Builder UI

av_server_plot_download()

Attach a Publication-Ready Figure Download to a Plot Card

av_server_report_builder()

Report Builder Server Logic