Struct GeneSets 

pub struct GeneSets {
    pub names: FxHashMap<Box<str>, Box<str>>,
    pub term_genes: FxHashMap<Box<str>, FxHashSet<Box<str>>>,
    pub gene_aliases: FxHashMap<Box<str>, FxHashSet<Box<str>>>,
}

A collection of gene-sets keyed by term id — the common form all sources (GAF/GMT/markers) reduce to before scoring.

Fields

names: FxHashMap<Box<str>, Box<str>>

term id → display name (absent ⇒ display the id itself).

term_genes: FxHashMap<Box<str>, FxHashSet<Box<str>>>

term id → member gene keys (upper-cased primary identifier).

gene_aliases: FxHashMap<Box<str>, FxHashSet<Box<str>>>

gene key → all identifier aliases for that gene (including the key), used to reconcile against an expression dictionary (HGNC / ENSG / UniProt).

Implementations

impl GeneSets

pub fn n_terms(&self) -> usize

Number of distinct terms (gene-sets).

pub fn n_annotations(&self) -> usize

Total membership entries summed over terms (post-propagation for GAF).

pub fn n_genes(&self) -> usize

Number of distinct member genes across all sets.

impl GeneSets

pub fn reconcile( &self, index: &GeneIndex, min_members: usize, max_members: Option<usize>, ) -> Reconciled

Reconcile each member gene against index (built over the expression dictionary), trying every identifier alias and taking the first hit, then keep only terms whose matched-member count is in [min_members, max_members]. The upper bound matters: GSEA es_std is ill-behaved for near-universal sets (their restandardization SD collapses → spurious huge z), so giant root-level terms must be excluded — the standard GSEA size window. max_members = None disables the cap. Handles HGNC / ENSG / ENSG_HGNC conventions via GeneIndex.

Trait Implementations

impl Default for GeneSets

fn default() -> Self

Returns the “default value” for a type.