LD Score-Based LD Statistic

Pre-computed LD scores for each SNP. Used by S-LDSC and g-LDSC. Supports both standard LD scores and annotation-stratified ones.

The scores and their regression weights are mcols rather than slots, because they are parallel to the variants: as slots they would survive a subset unchanged while the ranges narrowed, leaving scores describing variants that are no longer there.

An LdScore storing per-block LD matrices (ldMatrixList) cannot be subset or reordered: each block's matrix indexes its variants by position, so narrowing the variants would leave it describing other variants. A scores-only object, or one reading its LD from a genotype panel, subsets freely.

Slots

ldMatrixList

For g-LDSC: a list of per-block LD correlation (R) matrices used to compute the FGLS residual covariance, kept when the scores were built from LdMatrix blocks. Empty for a scores-only object, and for one built from a genotype panel, which reads each block's LD from the panel instead (see LdStatistic).