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Overlap QTL and GWAS top loci by allele-aware variant matching

Source: R/overlapTopLoci.R
overlapTopLoci.Rd

Intersect the top-loci tables of a QtlFineMappingResult and a GwasFineMappingResult on shared variants, matched with pecotmr's allele-aware matchVariants (handling strand flips / ref-alt swaps rather than naive id equality). The GWAS side is harmonized to the QTL orientation: its signed effect columns (beta, z, conditional_effect) are sign-flipped and its effect-allele frequency (af) is complemented wherever a swap occurred. The result keeps the variant key columns once (from the QTL, the reference orientation) and prefixes every other column qtl_ / gwas_. A variant shared across several QTL contexts and/or GWAS studies yields one row per (QTL entry x GWAS entry) pair (a wide cross-product per variant).

Usage

overlapTopLoci(qtl, gwas, ...)

# S4 method for class 'QtlFineMappingResult,GwasFineMappingResult'
overlapTopLoci(
  qtl,
  gwas,
  signalCutoff = 0.025,
  type = c("data.frame", "GRanges"),
  ...
)

Arguments

qtl

A QtlFineMappingResult.

gwas

A GwasFineMappingResult.

...

Ignored.

signalCutoff

PIP cutoff forwarded to getTopLoci for both inputs. Default 0.025.

type

"data.frame" (default) or "GRanges".

Value

A data.frame (or GRanges) keyed on the QTL variant (variant_id, chrom, pos, A1, A2) with all other columns prefixed qtl_ / gwas_. Zero rows when there is no allele-aware overlap.

See also

getTopLoci, matchVariants