GWAS Fine-Mapping Result Collection — QtlFineMappingResult • pecotmr

S4 collection of fine-mapping fits for one or more GWAS studies on a single LD block. Keyed by the identity tuple (study, method); each entry is a FineMappingEntry.

Required columns: study, method, entry. The 2-tuple is unique. The caller is expected to construct one GwasFineMappingResult per LD block (no in-class block indexing).

Construct a QtlFineMappingResult DFrame-subclass collection from per-tuple vectors and a list of FineMappingEntry payloads (one per tuple). The optional ldSketch slot records the LD reference used for RSS-derived fits; pass NULL (the default) for individual-level fits.

Usage

QtlFineMappingResult(
  study,
  context,
  trait,
  method,
  entry,
  jointStudies = NULL,
  jointContexts = NULL,
  jointTraits = NULL,
  region = NULL,
  traitPos = NULL,
  ldSketch = NULL
)

Arguments

study: Character vector of study identifiers (per tuple). Use the sentinel "joint" for rows produced by a cross-study joint fit.
context: Character vector of context labels (per tuple). Use "joint" for rows produced by a cross-context joint fit.
trait: Character vector of trait identifiers (per tuple). Use "joint" for rows produced by a cross-trait joint fit.
method: Character vector of fine-mapping method names (per tuple).
entry: List / SimpleList of FineMappingEntry objects.
jointStudies: Optional character vector (length length(study)) listing the semicolon-joined studies participating in each row's cross-study joint fit, or NA_character_ for non-joint rows. When NULL (default) the column is omitted.
jointContexts: Optional character vector for cross-context joints. Same shape as jointStudies.
jointTraits: Optional character vector for cross-trait joints. Same shape as jointStudies.
region: Optional GRanges (length length(study)) giving the genomic anchor of each row's trait (its own coordinates). Carried forward as provenance (e.g. for cTWAS LD-block placement); not part of the identity key. NULL (default) omits the column.
ldSketch: An optional GenotypeHandle (the LD reference for RSS-derived fits), or NULL for individual-level fits.

Value

A QtlFineMappingResult object.