A GwasFineMappingResult S4 collection holding
SuSiE-RSS fine-mapping output for de-identified GWAS summary statistics (one
study), fit over the same 2,828 variants as
qtlFineMappingExample so the two can be paired. Suitable as
the GWAS input to qtlEnrichmentPipeline. All variant
identifiers are synthetic. Built by
inst/scripts/prepare_example_data.R.
Format
A GwasFineMappingResult object: a
GRangesList-backed collection with one element (2,828 variants on
chr22) keyed by study_1 / susie, carrying the SuSiE-RSS fit
and a per-variant table with the standard post-processing columns
(pip, logBF, cs_95 / cs_70 / cs_50 and
their purities, marginal statistics). Four credible sets. ldSketch is
the bundled toy_canonical genotype panel, present
because qtlEnrichmentPipeline requires the GWAS collection to
carry one as its RSS-derived marker; the LD actually used for the fit is an
in-memory correlation matrix computed from eqtlRegionExample.
Examples
data(gwasFineMappingExample)
gwasFineMappingExample
#> GwasFineMappingResult: 1 entries
#> 1 studies, 1 methods
#> LD sketch: plink1 @ pecotmr://extdata/toy_canonical
head(getTopLoci(gwasFineMappingExample))
#> # A tibble: 6 × 27
#> study context trait blockId method variant_id chrom pos A1 A2 N
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <int> <chr> <chr> <dbl>
#> 1 study_1 NA NA region… susie chr22:323… chr22 3.23e7 T C NA
#> 2 study_1 NA NA region… susie chr22:323… chr22 3.24e7 G A NA
#> 3 study_1 NA NA region… susie chr22:323… chr22 3.24e7 G A NA
#> 4 study_1 NA NA region… susie chr22:323… chr22 3.24e7 C T NA
#> 5 study_1 NA NA region… susie chr22:323… chr22 3.24e7 G A NA
#> 6 study_1 NA NA region… susie chr22:323… chr22 3.24e7 A C NA
#> # ℹ 16 more variables: af <dbl>, beta <dbl>, se <dbl>, pip <dbl>, logBF <dbl>,
#> # cs_95 <chr>, cs_70 <chr>, cs_50 <chr>, cs_95_purity <dbl>,
#> # cs_70_purity <dbl>, cs_50_purity <dbl>, within_cs_pip <dbl>, gene <chr>,
#> # event <chr>, grange_start <int>, grange_end <int>