Example QTL Fine-Mapping Result Paired With the LD-Source Fixtures

A multi-credible-set QtlFineMappingResult whose SuSiE fit is over the SAME 200 synthetic variants (chr22, ~14.5 Mb) as the shipped LD sources qtlDatasetExample and qtlSumStatsExample. Unlike qtlFineMappingExample (fit over a different region than any shipped LD source), this fixture is self-consistent with those LD sources, so cross-object LD-derived computations such as computeCsCorrelation resolve against it. A phenotype with two causal variants in low mutual LD was simulated so the fit yields two credible sets. Built by inst/scripts/prepare_paired_finemapping_example.R.

Format

A QtlFineMappingResult object: a GRangesList-backed collection with one element (200 variants on chr22) keyed by study1 / context1 / gene1 / susie, carrying the SuSiE fit with two credible sets and a per-variant table with the standard post-processing columns (pip, logBF, cs_95 / cs_70 / cs_50 and their purities, marginal statistics).

Examples

data(qtlFineMappingPairedExample)
data(qtlSumStatsExample)
fe <- getFineMappingResult(qtlFineMappingPairedExample)
computeCsCorrelation(fe, qtlSumStatsExample)
#>             L2          L3
#> L2  1.00000000 -0.08404977
#> L3 -0.08404977  1.00000000