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Get a Single Summary-Statistic Entry or Embedded Collection

Source: R/AllGenerics.R, R/MultiStudyQtlDataset.R, R/qtlSumStats.R
getSumStats.Rd

Behavior depends on the class of x:

For GwasSumStats / QtlSumStats

Returns the per-variant GRanges of summary statistics for one entry, selected by its identity tuple (study for GWAS; study, context, trait for QTL).

For MultiStudyQtlDataset

Returns the embedded QtlSumStats collection (the summary-statistic-only studies), or NULL when absent. No selection arguments are accepted in this case.

Usage

getSumStats(x, ...)

# S4 method for class 'MultiStudyQtlDataset'
getSumStats(x, ...)

# S4 method for class 'QtlSumStats'
getSumStats(
  x,
  study = NULL,
  context = NULL,
  trait = NULL,
  annotateSignificance = NULL,
  ...
)

Arguments

x

A GwasSumStats, QtlSumStats, or MultiStudyQtlDataset object.

...

Class-specific selection arguments (see above).

annotateSignificance

Optional correction-method name ("permutation" / "bonferroni_original" / "bonferroni_filtered" / "qvalue"). When set on a QtlSumStats enriched by qtlAssociationPostprocess, a logical significant mcol for that method is added to the returned entry (the significance is derived on the fly, not stored). Flat export flattens this full entry GRanges (all mcols) directly; note getSumstatDf is a fixed GWAS-schema view and does not carry the association columns.

Value

A GRanges, a QtlSumStats, or NULL.