Enrichment and FDR

HiMaLAYAS tests enrichment across clusters and categorical annotations using a one-sided hypergeometric test. Multiple testing across cluster-term tests is controlled with Benjamini-Hochberg FDR.

Common Methods

Method	Description
analysis.enrich(...)	Runs one-sided hypergeometric enrichment over clustered labels and annotations.
analysis.finalize(...)	Attaches plotting layout and BH-FDR q-values to produce a plotting-ready Results.

enrich

Runs one-sided hypergeometric enrichment over clustered labels and annotations.

Analysis.enrich(
    *,
    min_overlap: int = 1,
    background: Matrix | None = None,
) -> Analysis

Parameters

Parameter	Type	Default	Description
min_overlap	int	1	Minimum overlap k to report. Increase to reduce weak hits.
background	Matrix | None	None	Optional background universe. If provided, must contain all matrix labels.

finalize

Attaches plotting layout and BH-FDR q-values to produce a plotting-ready Results. Call this before using Plotter.

Analysis.finalize(
    *,
    col_cluster: bool = False,
) -> Analysis

Parameters

Parameter	Type	Default	Description
col_cluster	bool	False	Computes a dendrogram-based column order for plotting using the same linkage_method, linkage_metric, and optimal_ordering set in Analysis.cluster(...).

Example

analysis = (
    Analysis(matrix, annotations)
    .cluster(...)
    .enrich(min_overlap=2)
    .finalize()
)

results = analysis.results

After running enrichment, the primary output is attached as:

Attribute	Type	Description
analysis.results	Results	Enrichment results table and attached context used for filtering, inspection, and plotting.

FDR Correction

HiMaLAYAS uses Benjamini-Hochberg (BH) FDR across cluster-term tests.

See Results and Filtering for examples of filtering on q-values.

Notes

• If no terms pass filtering, the results table is empty.