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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 tibble (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

Examples

data(qtlFineMappingLbfExample)
data(gwasFineMappingLbfExample)
overlapTopLoci(qtlFineMappingLbfExample, gwasFineMappingLbfExample)
#> # A tibble: 100 × 49
#>    variant_id         chrom      pos A1    A2    qtl_study qtl_context qtl_trait
#>    <chr>              <chr>    <int> <chr> <chr> <chr>     <chr>       <chr>    
#>  1 chr22:10416669:A:T chr22 10416669 T     A     test_stu… context1    ENSG0000…
#>  2 chr22:10424460:A:T chr22 10424460 T     A     test_stu… context1    ENSG0000…
#>  3 chr22:10443846:A:T chr22 10443846 T     A     test_stu… context1    ENSG0000…
#>  4 chr22:10456378:A:T chr22 10456378 T     A     test_stu… context1    ENSG0000…
#>  5 chr22:10456420:A:T chr22 10456420 T     A     test_stu… context1    ENSG0000…
#>  6 chr22:10475014:A:T chr22 10475014 T     A     test_stu… context1    ENSG0000…
#>  7 chr22:10499732:A:T chr22 10499732 T     A     test_stu… context1    ENSG0000…
#>  8 chr22:10500354:A:T chr22 10500354 T     A     test_stu… context1    ENSG0000…
#>  9 chr22:10525507:A:T chr22 10525507 T     A     test_stu… context1    ENSG0000…
#> 10 chr22:10528863:A:T chr22 10528863 T     A     test_stu… context1    ENSG0000…
#> # ℹ 90 more rows
#> # ℹ 41 more variables: qtl_blockId <chr>, qtl_method <chr>, qtl_N <dbl>,
#> #   qtl_af <dbl>, qtl_beta <dbl>, qtl_se <dbl>, qtl_pip <dbl>, qtl_logBF <dbl>,
#> #   qtl_cs_95 <chr>, qtl_cs_70 <chr>, qtl_cs_50 <chr>, qtl_cs_95_purity <dbl>,
#> #   qtl_cs_70_purity <dbl>, qtl_cs_50_purity <dbl>, qtl_within_cs_pip <dbl>,
#> #   qtl_gene <chr>, qtl_event <chr>, qtl_grange_start <int>,
#> #   qtl_grange_end <int>, gwas_study <chr>, gwas_context <chr>, …