LD Data Container — LdData-class • pecotmr

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.
genotypeHandle: A GenotypeHandle, a list of GenotypeHandles (for mixture panels), or NULL when only pre-computed R is available.
snpIdx: Integer vector of 1-based SNP indices into the handle's snpInfo. NULL when correlation is pre-computed.
variants: A GRanges object with variant metadata (A1, A2, variant_id, and optionally allele_freq, variance, n_nomiss).
blockMetadata: An LdBlocks object or a data.frame with block boundary information.
nRef: Integer, reference panel sample size.
mixtureWeights: NULL when genotypeHandle is a single GenotypeHandle; a numeric vector of mixing proportions (one per panel, summing to 1) when genotypeHandle is a list of GenotypeHandles. Used by getCorrelation() to compute a weighted-average mixture LD matrix; required whenever genotypeHandle is a list and getCorrelation() will be called.