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
credibleSets(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 reference: NULL (individual-level fit)
head(topLoci(qtlFineMappingExample))
#> GRanges object with 6 ranges and 31 metadata columns:
#> seqnames ranges strand | study context trait
#> <Rle> <IRanges> <Rle> | <character> <character> <character>
#> [1] chr22 32596246 * | study_1 context_1 gene_1
#> [2] chr22 32724254 * | study_1 context_1 gene_1
#> [3] chr22 32724508 * | study_1 context_1 gene_1
#> [4] chr22 32728910 * | study_1 context_1 gene_1
#> [5] chr22 32729588 * | study_1 context_1 gene_1
#> [6] chr22 32732510 * | study_1 context_1 gene_1
#> blockId method dataType dataSource standardized
#> <character> <character> <character> <character> <character>
#> [1] <NA> susie <NA> <NA> <NA>
#> [2] <NA> susie <NA> <NA> <NA>
#> [3] <NA> susie <NA> <NA> <NA>
#> [4] <NA> susie <NA> <NA> <NA>
#> [5] <NA> susie <NA> <NA> <NA>
#> [6] <NA> susie <NA> <NA> <NA>
#> variant_id chrom pos A1 A2
#> <character> <character> <integer> <character> <character>
#> [1] chr22:32596246:T:C chr22 32596246 C T
#> [2] chr22:32724254:T:C chr22 32724254 C T
#> [3] chr22:32724508:C:A chr22 32724508 A C
#> [4] chr22:32728910:G:A chr22 32728910 A G
#> [5] chr22:32729588:T:C chr22 32729588 C T
#> [6] chr22:32732510:G:A chr22 32732510 A G
#> N af posterior_effect posterior_se theta pip
#> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
#> [1] 415 NA -0.01284643 0.0324407 0 0.1444970
#> [2] 415 NA 0.00601338 0.0283820 0 0.0442663
#> [3] 415 NA 0.00601338 0.0283820 0 0.0442663
#> [4] 415 NA 0.00534990 0.0268018 0 0.0394963
#> [5] 415 NA 0.00464131 0.0249437 0 0.0345102
#> [6] 415 NA 0.00937127 0.0351058 0 0.0684514
#> logBF cs_95 cs_70 cs_50 cs_95_purity cs_70_purity
#> <numeric> <character> <character> <character> <numeric> <numeric>
#> [1] 6.53015 susie_0 susie_0 susie_0 0.000000 0.000000
#> [2] 15.67566 susie_1 susie_1 susie_1 0.625503 0.938229
#> [3] 15.67566 susie_1 susie_1 susie_1 0.625503 0.938229
#> [4] 15.56140 susie_1 susie_1 susie_0 0.625503 0.938229
#> [5] 15.42615 susie_1 susie_1 susie_0 0.625503 0.938229
#> [6] 16.11229 susie_1 susie_1 susie_1 0.625503 0.938229
#> cs_50_purity within_cs_pip gene event grange_start
#> <numeric> <numeric> <character> <character> <integer>
#> [1] 0.000000 NA <NA> <NA> <NA>
#> [2] 0.940595 0.0441714 <NA> <NA> <NA>
#> [3] 0.940595 0.0441714 <NA> <NA> <NA>
#> [4] 0.000000 0.0394021 <NA> <NA> <NA>
#> [5] 0.000000 0.0344176 <NA> <NA> <NA>
#> [6] 0.940595 0.0683547 <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