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. ldReference
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 reference: plink1 @ pecotmr://extdata/toy_canonical
head(topLoci(gwasFineMappingExample))
#> GRanges object with 6 ranges and 31 metadata columns:
#> seqnames ranges strand | study context trait
#> <Rle> <IRanges> <Rle> | <character> <character> <character>
#> [1] chr22 32337604 * | study_1 <NA> <NA>
#> [2] chr22 32350609 * | study_1 <NA> <NA>
#> [3] chr22 32354393 * | study_1 <NA> <NA>
#> [4] chr22 32362470 * | study_1 <NA> <NA>
#> [5] chr22 32362793 * | study_1 <NA> <NA>
#> [6] chr22 32369273 * | study_1 <NA> <NA>
#> blockId method dataType dataSource standardized
#> <character> <character> <character> <character> <character>
#> [1] region_1 susie <NA> <NA> <NA>
#> [2] region_1 susie <NA> <NA> <NA>
#> [3] region_1 susie <NA> <NA> <NA>
#> [4] region_1 susie <NA> <NA> <NA>
#> [5] region_1 susie <NA> <NA> <NA>
#> [6] region_1 susie <NA> <NA> <NA>
#> variant_id chrom pos A1 A2
#> <character> <character> <integer> <character> <character>
#> [1] chr22:32337604:C:T chr22 32337604 T C
#> [2] chr22:32350609:A:G chr22 32350609 G A
#> [3] chr22:32354393:A:G chr22 32354393 G A
#> [4] chr22:32362470:T:C chr22 32362470 C T
#> [5] chr22:32362793:A:G chr22 32362793 G A
#> [6] chr22:32369273:C:A chr22 32369273 A C
#> N af posterior_effect posterior_se theta pip
#> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
#> [1] NA NA 0.002119882 0.00433735 0 0.1968901
#> [2] NA NA 0.000792956 0.00281382 0 0.0751927
#> [3] NA NA 0.001375308 0.00361922 0 0.1288942
#> [4] NA NA 0.004781037 0.00552692 0 0.4367631
#> [5] NA NA 0.001452388 0.00370652 0 0.1359622
#> [6] NA NA 0.000270653 0.00166687 0 0.0262804
#> logBF cs_95 cs_70 cs_50 cs_95_purity cs_70_purity
#> <numeric> <character> <character> <character> <numeric> <numeric>
#> [1] 16782.2 susie_rss_3 susie_rss_3 susie_rss_3 0.984661 0.984661
#> [2] 16755.2 susie_rss_3 susie_rss_0 susie_rss_0 0.984661 0.000000
#> [3] 16919.3 susie_rss_3 susie_rss_0 susie_rss_0 0.984661 0.000000
#> [4] 16950.6 susie_rss_3 susie_rss_3 susie_rss_3 0.984661 0.984661
#> [5] 16766.3 susie_rss_3 susie_rss_3 susie_rss_0 0.984661 0.984661
#> [6] 21268.5 susie_rss_0 susie_rss_0 susie_rss_0 0.000000 0.000000
#> cs_50_purity within_cs_pip gene event grange_start
#> <numeric> <numeric> <character> <character> <integer>
#> [1] 0.987238 0.1968901 <NA> <NA> <NA>
#> [2] 0.000000 0.0751927 <NA> <NA> <NA>
#> [3] 0.000000 0.1288942 <NA> <NA> <NA>
#> [4] 0.987238 0.4367631 <NA> <NA> <NA>
#> [5] 0.000000 0.1359622 <NA> <NA> <NA>
#> [6] 0.000000 NA <NA> <NA> <NA>
#> grange_end
#> <integer>
#> [1] <NA>
#> [2] <NA>
#> [3] <NA>
#> [4] <NA>
#> [5] <NA>
#> [6] <NA>
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths