Create a QtlFineMappingResult Collection

Construct a QtlFineMappingResult DFrame-subclass collection from per-tuple vectors and a list of FineMappingRow 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,
  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 FineMappingRow 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.

traitPos

Optional per-row trait genomic anchor (a GRanges or NULL), carried forward as provenance; not part of the identity key. NULL (default) omits the column.

ldSketch

An optional genotype panel (see readGenotypes) (the LD reference for RSS-derived fits), or NULL for individual-level fits.

Value

A QtlFineMappingResult object.

Examples

tl <- data.frame(variant_id = paste0("chr1:", 100 * 1:3, ":A:G"),
  pip = c(0.9, 0.5, 0.1), cs = c(1L, 1L, NA))
fe <- fineMappingRow(
  variantIds = tl$variant_id, susieFit = list(), topLoci = tl)
QtlFineMappingResult(study = "s1", context = "brain", trait = "g1",
  method = "susie", entry = list(fe))
#> QtlFineMappingResult: 1 entries
#>   1 studies, 1 contexts, 1 traits, 1 methods
#>   LD sketch: NULL (individual-level fit)