Per-sample gene-set scoring with GSVA

Internal function that runs Gene Set Variation Analysis (gsva) on an expression matrix using the cached CTD chemical gene sets. Unlike ORA/GSEA/CAMERA — which return a single p-value per chemical (group-level inference) — GSVA produces a matrix of per-sample enrichment scores: one row per chemical, one column per sample. These scores are suitable for downstream clustering, association tests against phenotypes, survival analysis, or heatmap visualization.

Usage

.run_gsva(expr, id_type = NULL, cache_dir, interaction_types = NULL, ...)

Arguments

expr

Numeric expression matrix (genes x samples). rownames(expr) must be Entrez IDs or HGNC symbols matching the cached CTD gene sets.

id_type

Either "entrez", "symbol", or NULL for auto-detection from rownames(expr).

cache_dir

Directory holding the cached CTD .rda files.

...

Forwarded to gsvaParam (e.g. kcdf, minSize, maxSize, tau, maxDiff).

Value

A numeric matrix of GSVA enrichment scores with CTD chemical IDs in rows and samples in columns.