A QtlFineMappingResult S4 collection holding SuSiE
fine-mapping output for de-identified individual-level eQTL data, for a
single
(study, context, trait) tuple. Suitable as the QTL input to
qtlEnrichmentPipeline. All variant identifiers and
region/context names are synthetic.
Format
A QtlFineMappingResult object: a
GRangesList-backed collection with one element (2,828 variants on
chr22) keyed by study_1 / context_1 / gene_1 /
susie, carrying the SuSiE 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).
One credible set of 42 variants. Its min.abs.corr is 0.626, below the
pipeline default of 0.8, so the fixture was built at minAbsCorr = 0.5
to keep the set labelled; cs_95_purity records the true value, so
getCs(x, minPurity = 0.8) still filters it out. Built by
inst/scripts/prepare_example_data.R.
Examples
data(qtlFineMappingExample)
qtlFineMappingExample
#> QtlFineMappingResult: 1 entries
#> 1 studies, 1 contexts, 1 traits, 1 methods
#> LD sketch: NULL (individual-level fit)
head(getTopLoci(qtlFineMappingExample))
#> # 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 contex… gene… NA susie chr22:325… chr22 3.26e7 C T 415
#> 2 study_1 contex… gene… NA susie chr22:327… chr22 3.27e7 C T 415
#> 3 study_1 contex… gene… NA susie chr22:327… chr22 3.27e7 A C 415
#> 4 study_1 contex… gene… NA susie chr22:327… chr22 3.27e7 A G 415
#> 5 study_1 contex… gene… NA susie chr22:327… chr22 3.27e7 C T 415
#> 6 study_1 contex… gene… NA susie chr22:327… chr22 3.27e7 A G 415
#> # 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>