Summary Statistics Base Class

Virtual base class for QTL and GWAS summary statistics collections. Concrete subclasses (QtlSumStats, GwasSumStats) inherit from RangedTupleList and share the ldReference / qcInfo slots, and the genome build in seqinfo().

Each element is the per-variant GRanges of one tuple, so x[[i]] is that tuple's summary statistics and the identity columns live in mcols(x). There is no entry column: what used to be x$entry[[i]] is now simply x[[i]].

Slots

ldReference

The LD reference the collection was harmonized against and every pipeline reads LD from: a genotype panel (see readGenotypes), a GenotypeMixture or an LdMatrix, or NULL. Optional: LD-free workflows (e.g. mash, which operates across conditions per variant) carry NULL; pipelines that need LD validate its presence when they consume the collection.

qcInfo

A list recording which QC steps ran. Empty list() on construction; populated by summaryStatsQc() with a per-step audit record (filter names, drop counts, liftover target, RAISS settings, etc.). Fine-mapping and TWAS-weights pipelines reject inputs where length(qcInfo(x)) == 0L – the slot serves as both the gating flag and the audit trail.