LD Statistic (Virtual Base Class)

Abstract container for pre-computed LD statistics. Subclasses provide method-specific representations: eigendecompositions (for LDER/HDL/sHDL) and LD score matrices (for S-LDSC/g-LDSC).

An LdStatistic is a GRanges of the reference variants: one range per SNP, with SNP / A1 / A2 (and optionally MAF) in mcols. Per-variant statistics live in mcols too, so subsetting narrows the ranges and the statistics together. The genome build comes from seqinfo() rather than a slot of its own.

Slots

ldBlocks

A GRanges of LD block intervals.

nRef

Integer, sample size of the LD reference panel.

inSample

Logical, whether the LD reference is from the same cohort as the GWAS (affects bias correction).