LOLA enrichment (Wasm)

Wasm bindings for gtars-lola — LOLA (Locus Overlap Analysis) enrichment testing, runnable entirely in the browser. Given a user set of regions, a universe, and a region database (built in memory from API-served BED data), computes Fisher's exact test enrichment of the user set against every database region set.

See the Rust gtars-lola reference for the full statistical details — Fisher's exact test via hypergeometric survival function, CMLE odds ratio, contingency table semantics, and compatibility notes with R LOLA. This page is a Wasm-focused binding reference.

In-memory only — no folder loading

The Wasm binding's LolaRegionDB is built entirely from in-memory data ({regions, name} entries passed in at construction). The Rust RegionDB::from_lola_folder loader is not available in Wasm — it requires a filesystem. In practice you'd fetch the region database from an API and pass the regions directly into the constructor, or build it from a pre-indexed IGD on the server side.

Import

import init, {
  LolaRegionDB,
  runLOLA,
  checkUniverseAppropriateness,
} from '@databio/gtars';

await init();

`LolaRegionDB`

Construction

Construct from an array of { regions, name } objects, where regions is an array of [chr, start, end] tuples and name is the filename-like identifier:

const dbEntries = [
  {
    name: 'encode_k562_ctcf.bed',
    regions: [
      ['chr1', 100, 200],
      ['chr1', 400, 500],
      ['chr2', 1000, 1100],
    ],
  },
  {
    name: 'encode_hela_ctcf.bed',
    regions: [
      ['chr1', 150, 250],
      ['chr2', 1050, 1150],
    ],
  },
];

const db = new LolaRegionDB(dbEntries);

The constructor builds an IGD overlap index internally and wraps it with minimal annotation (filename only). To attach richer per-file metadata — cell type, tissue, antibody, etc. — build the annotated RegionDB on the Rust side and serve it through a different transport (e.g. a custom binary format), or expose a method that accepts RegionSetAnno objects alongside the regions.

Accessors

db.numRegionSets              // number
db.listRegionSets()           // string[] — filenames
db.collectionAnno             // Array of { collectionname, collector, date, source, description } (empty for an in-memory DB)

// Extract region sets by 0-based index as a RegionSetList
// (pass null for "all sets"; names are populated from filenames)
const rsl = db.getRegionSets(null);
const rsl2 = db.getRegionSets([0, 5, 12]);

getRegionSets() returns a RegionSetList with .names populated from the database filenames.

`runLOLA`

Runs Fisher's exact test for every (user_set, db_set) pair and returns a column-oriented object suitable for dropping directly into a DataFrame or table.

runLOLA(
  userSets: Array<Array<[string, number, number]>>,
  universe: Array<[string, number, number]>,
  regionDb: LolaRegionDB,
  minOverlap?: number,       // default 1
  direction?: string,         // "enrichment" (default) | "depletion"
): LolaResultColumnar

Parameters: - userSets — array of user sets, where each user set is an array of [chr, start, end] tuples. Pass a single-element outer array [peaks] for a one-user-set analysis. - universe — a single array of [chr, start, end] tuples representing the background. - regionDb — a LolaRegionDB. - minOverlap — minimum bp overlap to count as overlapping (default 1). - direction — "enrichment" (default, P(X ≥ a), alternative "greater") or "depletion" (P(X ≤ a), alternative "less"). "less" is accepted as an alias for depletion; any other value (including "greater") runs enrichment.

Returns an object with parallel arrays (one entry per (user_set, db_set) pair) using camelCase keys:

key	type	meaning
`userSet`	`number[]`	0-based user-set index
`dbSet`	`number[]`	0-based db-set index
`collection`	`(string \\| null)[]`	per-file annotation, usually null in Wasm
`pValueLog`	`number[]`	`-log10(p)` from Fisher's exact test, capped at ~322
`oddsRatio`	`number[]`	CMLE odds ratio (matches R `fisher.test()$estimate`)
`support`	`number[]`	overlap count between user set and db set
`rnkPv`, `rnkOr`, `rnkSup`	`number[]`	1-based per-metric ranks within the user set
`maxRnk`	`number[]`	max of the three ranks
`meanRnk`	`number[]`	mean of the three ranks
`b`, `c`, `d`	`number[]`	signed contingency values (can be negative)
`qValue`	`(number \\| null)[]`	BH-adjusted p-value (applied automatically inside `runLOLA`)
`description`, `cellType`, `tissue`, `antibody`, `treatment`, `dataSource`	`(string \\| null)[]`	per-file metadata
`filename`	`string[]`	db set file name
`size`	`number[]`	number of regions in the db set

Like the Python binding, Wasm runLOLA auto-applies annotate_results + apply_fdr_correction internally — you don't need to call them separately. Rows come back sorted by descending pValueLog, then ascending meanRnk (matching R LOLA output order).

Usage example

import init, {
  LolaRegionDB,
  runLOLA,
  RegionSet,
} from '@databio/gtars';

await init();

// Helper to convert a RegionSet to the tuple form LOLA expects
function toTuples(rs: RegionSet): Array<[string, number, number]> {
  // Iterate rs and pull chr/start/end — or keep the original BedEntries
  // if you still have them in scope from constructing the RegionSet.
  // ...
}

// 1. Build the region database from API-fetched data
const dbEntries = await fetchDatabaseRegions();  // [{ name, regions }, ...]
const db = new LolaRegionDB(dbEntries);

// 2. Prepare user sets and universe as tuple arrays
const userSets = [userPeakTuples];
const universe = universeTuples;

// 3. Run enrichment
const results = runLOLA(userSets, universe, db, 1, 'enrichment');

// 4. Pivot to row-oriented view for rendering
const n = results.pValueLog.length;
for (let i = 0; i < n; i++) {
  console.log(
    `${results.filename[i]}  ` +
    `p=${results.pValueLog[i].toFixed(2)}  ` +
    `OR=${results.oddsRatio[i].toFixed(2)}  ` +
    `support=${results.support[i]}`
  );
}

Negative contingency values

If your user set contains regions outside the universe, the contingency table produces negative b/c/d. The binding matches R LOLA's behavior — it logs a warning, stores the signed values, and returns pValueLog = 0.0, oddsRatio = NaN for that row. Pre-process with checkUniverseAppropriateness (below) to detect this before running enrichment.

`checkUniverseAppropriateness`

Diagnostic check — for each user set, reports what fraction of user-set regions overlap the universe and whether there are many-to-many mappings.

const report = checkUniverseAppropriateness(userSets, universe);
// Returns a column-oriented object:
// {
//   userSet: number[],
//   totalRegions: number[],
//   regionsInUniverse: number[],
//   coverage: number[],        // 0.0 to 1.0 per user set
//   manyToMany: number[],      // count of user regions overlapping >1 universe region
//   warnings: string[]         // free-form warning messages, pooled across user sets
// }

const n = report.userSet.length;
for (let i = 0; i < n; i++) {
  console.log(
    `user set ${report.userSet[i]}: ` +
    `${(report.coverage[i] * 100).toFixed(1)}% coverage, ` +
    `${report.manyToMany[i]} many-to-many`
  );
}
for (const w of report.warnings) {
  console.warn('⚠', w);
}

Warnings fire when coverage drops below 50% (severe) or 90% (moderate), or when any user region overlaps more than one universe region.

Rust-only helpers not exposed in Wasm

The Rust universe module has two additional helpers — redefine_user_sets (rewrite user sets in terms of universe regions) and build_restricted_universe (disjoint union of all user sets, for differential analysis). Neither is currently exposed in the Wasm binding. If you need them, you can replicate the logic client-side using RegionSetList operations from wasm/regionset, or request a binding.

LOLA enrichment (Wasm)

Import

LolaRegionDB

Construction

Accessors

runLOLA

Usage example

checkUniverseAppropriateness

See also

`LolaRegionDB`

`runLOLA`

`checkUniverseAppropriateness`