Genomic Annotation Matrix

Container for SNP-level annotations used in stratified heritability analysis. Supports binary (0/1) and continuous annotations. Annotations are classified as baseline (always jointly fitted) or candidate (evaluated via score statistics).

Slots

snpRanges

A GRanges object with one range per SNP, defining genomic positions.

annotations

A numeric matrix (SNPs x annotations). Dense for small annotation counts, can be sparse (dgCMatrix) for large binary annotation sets.

annotationMeta

A data.frame with columns:

name

Character, annotation name

tier

Character, one of "baseline" or "candidate"

type

Character, one of "binary" or "continuous"

genome

Character string for genome build.