Explore AlphaGenome Variant Scores — av

The main entry point for AlphaVaR analysis. Imports a CSV file from AlphaGenome, computes enrichment statistics, and launches an interactive Shiny explorer.

Usage

av_explore(file, max_upload_mb = 500)

Arguments

file: Path to an AlphaGenome variant scores CSV file.
max_upload_mb: Numeric. Maximum file upload size in megabytes (default 500). Passed through to av_run_shiny.

Value

This function does not return; it interrupts R execution to run the app.

Examples

example_file <- system.file(
  "extdata", "bcl11a_rs1427407_example.csv",
  package = "AlphaVaR"
)

# The two preparation steps av_explore() performs before it hands the object
# to the app:
obj <- av_import_csv(example_file)
#> Reading bcl11a_rs1427407_example.csv ...
obj <- av_calc_enrichment(obj)
print(obj)
#> === AlphaVarSet Object ===
#> Entries:    2,676 
#> Variants:   2 
#> Modalities: 11 
#> Columns:    25 (incl. 19 extra)
#> Score Mode: quantile_score 
#> Source:     bcl11a_rs1427407_example.csv 
#> Computed:   comparisons 

# The launch itself starts a Shiny server and blocks the session.
if (interactive()) {
  av_explore(example_file)

  av_explore(example_file, max_upload_mb = 1000)
}