LD Data Container

S4 container for LD information. Stores either a pre-computed correlation matrix or a GenotypeHandle (or list of handles for mixture panels) for lazy genotype/correlation access.

Slots

correlation

A correlation matrix, a list of per-block matrices (block-diagonal LD), or NULL if genotypes are available and R should be computed on demand.

genotype_handle

A GenotypeHandle, a list of GenotypeHandles (for mixture panels), or NULL when only pre-computed R is available.

snp_idx

Integer vector of 1-based SNP indices into the handle's snp_info. NULL when correlation is pre-computed.

variants

A GRanges object with variant metadata (A1, A2, variant_id, and optionally allele_freq, variance, n_nomiss).

block_metadata

An LDBlocks object or a data.frame with block boundary information.

n_ref

Integer, reference panel sample size.