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Create a QtlFineMappingResult Collection

Source: R/QtlFineMappingResult.R
QtlFineMappingResult.Rd

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

Usage

QtlFineMappingResult(
  studyName,
  context,
  trait,
  method,
  entry,
  jointStudies = NULL,
  jointContexts = NULL,
  jointTraits = NULL,
  traitPos = NULL,
  region = NULL,
  dataType = NULL,
  dataSource = NULL,
  weightStandardized = NULL,
  ldReference = NULL
)

Arguments

studyName

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.

region

Optional per-row analysis WINDOW (a GRanges or NULL) – the interval each row's fit was run over, carried forward as provenance; not part of the identity key. NULL (default) omits the column, and genomicRegion then derives the window from the span of the variants present.

dataType

Optional assay / modality label ("bulk_rnaseq", "methylation"), recorded as a per-row provenance column. Length 1 or one per row; NULL (default) omits the column.

dataSource

Optional per-row label for the kind of input the fit saw, "individual" or "sumstat". Recorded rather than derived: a combined collection can hold rows of both kinds, and its single ldReference cannot say which row came from which.

weightStandardized

Optional per-row flag: whether the posterior effect is on the STANDARDIZED genotype scale. The posterior effect IS the prediction weight, so it carries the same scale question as a TWAS weight. fineMappingPipeline always passes TRUE: it standardizes genotypes before fitting, and the posterior mean is reported on the scale of the X the fit was given. The argument exists for a collection assembled by hand, where only the caller knows.

ldReference

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(studyName = "s1", context = "brain", trait = "g1",
  method = "susie", entry = list(fe))
#> QtlFineMappingResult: 1 entries
#>   1 studies, 1 contexts, 1 traits, 1 methods
#>   LD reference: NULL (individual-level fit)