Create a QtlSumStats Collection Object — QtlSumStats • pecotmr

Construct a QtlSumStats S4 DFrame-subclass collection from per-tuple vectors and a list of GRanges entries (one per tuple), plus a single LD sketch handle and a single genome build that apply to the whole collection. Each GRanges entry must carry per-variant statistics in its mcols (SNP, A1, A2, Z, N; plus optional MAF, INFO, BETA, SE, P).

Usage

QtlSumStats(
  study,
  context,
  trait,
  entry,
  genome,
  ldSketch = NULL,
  varY = NA_real_,
  qcInfo = list(),
  traitPos = NULL,
  ...
)

Arguments

study: Character vector of study identifiers (per tuple).
context: Character vector of context labels (per tuple).
trait: Character vector of trait identifiers (per tuple).
entry: A list / SimpleList of GRanges, one per tuple. Same length as study, context, and trait.
genome: Single character string giving the genome build (e.g., "hg19", "hg38"). Uniform across the collection because all entries share the same LD sketch.
ldSketch: A GenotypeHandle carrying the LD reference.
varY: Optional numeric vector of per-tuple phenotype variances (NA_real_ entries allowed).
...: Additional per-tuple columns to attach to the collection.

Value

A QtlSumStats object.