Create a GwasSumStats Collection Object — GwasSumStats • pecotmr

Construct a GwasSumStats S4 DFrame-subclass collection from per-study tuple vectors and a list of GRanges entries (one per study), 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 (at minimum SNP, A1, A2, Z, N; optionally MAF, INFO, BETA, SE, P).

Usage

GwasSumStats(
  study,
  entry,
  genome,
  ldSketch = NULL,
  varY = NA_real_,
  nCase = NULL,
  nControl = NULL,
  qcInfo = list(),
  ...
)

Arguments

study: Character vector of study identifiers (must be unique).
entry: A SimpleList or list of GRanges, one per study.
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-study phenotype variances (NA_real_ entries allowed). Used by the sufficient-statistic interface; z-score RSS analyses should leave entries as NA.
nCase, nControl: Optional per-study case / control counts. The columns are attached only when supplied (default NULL), so quantitative-trait collections keep the original schema. When given, pass length 1 or length(study) (use NA for the non-case/control studies in a mixed collection). For case/control GWAS, downstream consumers (e.g. colocboostPipeline) use the effective sample size 4 / (1/nCase + 1/nControl) in place of the per-variant N.
...: Additional per-study columns to attach to the collection.

Value

A GwasSumStats object.